# Notebook from czbiohub/kh-analysis
Path: notebooks/500_qfo_download.ipynb

folder = '/home/olga/data_sm/kmer-hashing/quest-for-orthologs/data/2019'
! mkdir -p $foldermkdir: cannot create directory ‘/home/olga/data_sm/kmer-hashing/quest-for-orthologs’: Permission denied
cd $folder/mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019
! wget ftp://ftp.ebi.ac.uk/pub/databases/reference_proteomes/QfO/QfO_release_2019_04.tar.gz--2019-12-25 17:50:13--  ftp://ftp.ebi.ac.uk/pub/databases/reference_proteomes/QfO/QfO_release_2019_04.tar.gz
           => ‘QfO_release_2019_04.tar.gz’
Resolving ftp.ebi.ac.uk (ftp.ebi.ac.uk)... 193.62.197.74
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/databases/reference_proteomes/QfO ... done.
==> SIZE QfO_release_2019_04.tar.gz ... 2704585887
==> PASV ... done.    ==> RETR QfO_release_2019_04.tar.gz ... done.
Length: 2704585887 (2.5G) (unauthoritative)

QfO_release_2019_04 100%[===================>]   2.52G   533KB/s    in 57m 27s

2019-12-25 18:47:42 (766 KB/s) - ‘QfO_release_2019_04.tar.gz’ saved [2704585887]

! tar xzvf QfO_release_2019_04.tar.gzREADME
Archaea/
Archaea/UP000001974_273057.idmapping
Archaea/UP000001686_374847.idmapping
Archaea/UP000000792_436308.fasta
Archaea/UP000000554_64091_DNA.miss
Archaea/UP000000792_436308.idmapping
Archaea/UP000000554_64091.idmapping
Archaea/UP000001686_374847.gene2acc
Archaea/UP000000554_64091.fasta
Archaea/UP000001686_374847.fasta
Archaea/UP000001686_374847_DNA.fasta
Archaea/UP000000554_64091.gene2acc
Archaea/UP000000792_436308.gene2acc
Archaea/UP000001686_374847.xml
Archaea/UP000000792_436308.xml
Archaea/UP000000536_69014.xml
Archaea/UP000000554_64091.xml
Archaea/UP000000805_243232.xml
Archaea/UP000001974_273057.xml
Archaea/UP000002487_188937.xml
Archaea/UP000000792_436308_DNA.fasta
Archaea/UP000002487_188937_DNA.miss
Archaea/UP000000805_243232_DNA.miss
Archaea/UP000001974_273057_DNA.miss
Archaea/UP000002487_188937.fasta
Archaea/UP000002487_188937_DNA.fasta
Archaea/UP000000805_243232.gene2acc
Archaea/UP000000536_69014_DNA.fasta
Archaea/UP000001974_273057_DNA.fasta
Archaea/UP000000805_243232_DNA.fasta
Archaea/UP000000536_69014.fasta
Archaea/UP000000805_243232.fasta
Archaea/UP000002487_188937.idmapping
Archaea/UP000000536_69014.idmapping
Archaea/UP000000536_69014.gene2acc
Archaea/UP000000805_243232.idmapping
Archaea/UP000002487_188937.gene2acc
Archaea/UP000001974_273057.fasta
Archaea/UP000001974_273057.gene2acc
Archaea/UP000000554_64091_DNA.fasta
Bacteria/
Bacteria/UP000001584_83332_additional.fasta
Bacteria/UP000001025_243090.gene2acc
Bacteria/UP000002526_224911.gene2acc
Bacteria/UP000001584_83332_DNA.miss
Bacteria/UP000002526_224911.idmapping
Bacteria/UP000001973_100226.gene2acc
Bacteria/UP000002526_224911.fasta
Bacteria/UP000000625_83333.gene2acc
Bacteria/UP000002526_224911_DNA.fasta
Bacteria/UP000001025_243090_DNA.fasta
Bacteria/UP000001025_243090.fasta
Bacteria/UP000001584_83332_DNA.fasta
Bacteria/UP000001425_1111708.gene2acc
Bacteria/UP000001025_243090.idmapping
Bacteria/UP000001425_1111708.idmapping
Bacteria/UP000001414_226186.fasta
Bacteria/UP000002524_243230.idmapping
Bacteria/UP000000577_243231_DNA.miss
Bacteria/UP000002524_243230.fasta
Bacteria/UP000001425_1111708_DNA.fasta
Bacteria/UP000002524_243230_DNA.miss
Bacteria/UP000000431_272561.idmapping
Bacteria/UP000007719_515635.fasta
Bacteria/UP000001425_1111708_DNA.miss
Bacteria/UP000000577_243231.fasta
Bacteria/UP000001973_100226.fasta
Bacteria/UP000007719_515635_DNA.fasta
Bacteria/UP000000577_243231.idmapping
Bacteria/UP000002524_243230.gene2acc
Bacteria/UP000000577_243231.gene2acc
Bacteria/UP000007719_515635.gene2acc
Bacteria/UP000001425_1111708.fasta
Bacteria/UP000002524_243230_DNA.fasta
Bacteria/UP000000577_243231_DNA.fasta
Bacteria/UP000000431_272561_DNA.fasta
Bacteria/UP000001570_224308_DNA.miss
Bacteria/UP000000431_272561_DNA.miss
Bacteria/UP000000431_272561.gene2acc
Bacteria/UP000000431_272561.fasta
Bacteria/UP000007719_515635.idmapping
Bacteria/UP000001570_224308.fasta
Bacteria/UP000000798_224324_DNA.fasta
Bacteria/UP000000798_224324_DNA.miss
Bacteria/UP000000798_224324.idmapping
Bacteria/UP000001570_224308.gene2acc
Bacteria/UP000001570_224308.idmapping
Bacteria/UP000000798_224324.fasta
Bacteria/UP000001570_224308_DNA.fasta
Bacteria/UP000002438_208964.fasta
Bacteria/UP000002438_208964_DNA.miss
Bacteria/UP000000798_224324.gene2acc
Bacteria/UP000002438_208964_additional.fasta
Bacteria/UP000002438_208964_DNA.fasta
Bacteria/UP000000807_243273.gene2acc
Bacteria/UP000000429_85962.fasta
Bacteria/UP000002438_208964.gene2acc
Bacteria/UP000000807_243273_DNA.miss
Bacteria/UP000008183_243274_DNA.miss
Bacteria/UP000001408_189518.gene2acc
Bacteria/UP000000807_243273_DNA.fasta
Bacteria/UP000008183_243274_DNA.fasta
Bacteria/UP000002438_208964.idmapping
Bacteria/UP000000807_243273.idmapping
Bacteria/UP000008183_243274.idmapping
Bacteria/UP000000807_243273.fasta
Bacteria/UP000000429_85962.gene2acc
Bacteria/UP000008183_243274.gene2acc
Bacteria/UP000001408_189518_DNA.miss
Bacteria/UP000001408_189518.fasta
Bacteria/UP000000429_85962.idmapping
Bacteria/UP000000429_85962_DNA.fasta
Bacteria/UP000001408_189518_DNA.fasta
Bacteria/UP000008183_243274.fasta
Bacteria/UP000000557_251221_DNA.miss
Bacteria/UP000000557_251221.gene2acc
Bacteria/UP000000425_122586_DNA.fasta
Bacteria/UP000000557_251221_DNA.fasta
Bacteria/UP000001584_83332.fasta
Bacteria/UP000000557_251221.fasta
Bacteria/UP000000557_251221.idmapping
Bacteria/UP000001408_189518.idmapping
Bacteria/UP000000425_122586_DNA.miss
Bacteria/UP000000425_122586.fasta
Bacteria/UP000000425_122586.gene2acc
Bacteria/UP000002521_190304.gene2acc
Bacteria/UP000002521_190304_DNA.miss
Bacteria/UP000002521_190304_DNA.fasta
Bacteria/UP000000425_122586.idmapping
Bacteria/UP000000718_289376_DNA.fasta
Bacteria/UP000000718_289376.gene2acc
Bacteria/UP000002521_190304.fasta
Bacteria/UP000002521_190304.idmapping
Bacteria/UP000000718_289376.idmapping
Bacteria/UP000002008_324602.gene2acc
Bacteria/UP000000718_289376.fasta
Bacteria/UP000002008_324602.idmapping
Bacteria/UP000002008_324602_DNA.fasta
Bacteria/UP000002008_324602.fasta
Bacteria/UP000002524_243230.xml
Bacteria/UP000000577_243231.xml
Bacteria/UP000001025_243090.xml
Bacteria/UP000001414_226186.xml
Bacteria/UP000002526_224911.xml
Bacteria/UP000000807_243273.xml
Bacteria/UP000008183_243274.xml
Bacteria/UP000007719_515635.xml
Bacteria/UP000000431_272561.xml
Bacteria/UP000000429_85962.xml
Bacteria/UP000002521_190304.xml
Bacteria/UP000000798_224324.xml
Bacteria/UP000001425_1111708.xml
Bacteria/UP000001408_189518.xml
Bacteria/UP000001973_100226_additional.fasta
Bacteria/UP000001973_100226_DNA.fasta
Bacteria/UP000001973_100226.idmapping
Bacteria/UP000000625_83333_additional.fasta
Bacteria/UP000001584_83332.idmapping
Bacteria/UP000000625_83333.idmapping
Bacteria/UP000001414_226186.gene2acc
Bacteria/UP000000625_83333_DNA.fasta
Bacteria/UP000001414_226186_DNA.fasta
Bacteria/UP000000625_83333_DNA.miss
Bacteria/UP000001584_83332.gene2acc
Bacteria/UP000000625_83333.fasta
Bacteria/UP000001414_226186.idmapping
Bacteria/UP000001570_224308_additional.fasta
Bacteria/UP000000557_251221.xml
Bacteria/UP000001584_83332.xml
Bacteria/UP000002438_208964.xml
Bacteria/UP000001570_224308.xml
Bacteria/UP000002008_324602.xml
Bacteria/UP000000718_289376.xml
Bacteria/UP000001973_100226.xml
Bacteria/UP000000425_122586.xml
Bacteria/UP000000625_83333.xml
Eukaryota/
Eukaryota/UP000008783_418459_DNA.fasta
Eukaryota/UP000005640_9606_DNA.fasta
Eukaryota/UP000002485_284812.gene2acc
Eukaryota/UP000005640_9606_additional.fasta
Eukaryota/UP000002485_284812_DNA.miss
Eukaryota/UP000059680_39947.idmapping
Eukaryota/UP000002494_10116_DNA.miss
Eukaryota/UP000059680_39947_DNA.fasta
Eukaryota/UP000001038_8090_additional.fasta
Eukaryota/UP000006727_3218_DNA.fasta
Eukaryota/UP000002494_10116_DNA.fasta
Eukaryota/UP000002254_9615_DNA.miss
Eukaryota/UP000059680_39947_DNA.miss
Eukaryota/UP000000542_5664_DNA.fasta
Eukaryota/UP000005640_9606_gcoord.miss
Eukaryota/UP000005640_9606_gcoord.xml
Eukaryota/UP000002485_284812_additional.fasta
Eukaryota/UP000006727_3218.idmapping
Eukaryota/UP000002494_10116.idmapping
Eukaryota/UP000015101_6412.idmapping
Eukaryota/UP000059680_39947.fasta
Eukaryota/UP000002254_9615.fasta
Eukaryota/UP000002494_10116_gcoord.xml
Eukaryota/UP000059680_39947.gene2acc
Eukaryota/UP000000437_7955.gene2acc
Eukaryota/UP000002485_284812_DNA.fasta
Eukaryota/UP000002195_44689.gene2acc
Eukaryota/UP000002485_284812.fasta
Eukaryota/UP000000437_7955_DNA.fasta
Eukaryota/UP000002485_284812.idmapping
Eukaryota/UP000015101_6412.fasta
Eukaryota/UP000015101_6412_DNA.fasta
Eukaryota/UP000015101_6412.gene2acc
Eukaryota/UP000002254_9615_DNA.fasta
Eukaryota/UP000000437_7955.fasta
Eukaryota/UP000002195_44689.fasta
Eukaryota/UP000002254_9615.gene2acc
Eukaryota/UP000006727_3218.fasta
Eukaryota/UP000015101_6412_gcoord.xml
Eukaryota/UP000002195_44689_additional.fasta
Eukaryota/UP000008783_418459.gene2acc
Eukaryota/UP000002254_9615.idmapping
Eukaryota/UP000000437_7955.idmapping
Eukaryota/UP000002195_44689_DNA.miss
Eukaryota/UP000002254_9615_gcoord.xml
Eukaryota/UP000002195_44689_DNA.fasta
Eukaryota/UP000008783_418459.fasta
Eukaryota/UP000002195_44689.idmapping
Eukaryota/UP000001038_8090_DNA.fasta
Eukaryota/UP000006727_3218_additional.fasta
Eukaryota/UP000000437_7955_DNA.miss
Eukaryota/UP000006727_3218.gene2acc
Eukaryota/UP000007266_7070.gene2acc
Eukaryota/UP000008783_418459.idmapping
Eukaryota/UP000001038_8090_DNA.miss
Eukaryota/UP000002149_214684_DNA.fasta
Eukaryota/UP000000542_5664.fasta
Eukaryota/UP000008143_8364_DNA.fasta
Eukaryota/UP000001038_8090.fasta
Eukaryota/UP000001357_81824_DNA.fasta
Eukaryota/UP000001038_8090.idmapping
Eukaryota/UP000001593_45351_DNA.fasta
Eukaryota/UP000000437_7955_gcoord.xml
Eukaryota/UP000000542_5664.idmapping
Eukaryota/UP000001300_284591.idmapping
Eukaryota/UP000001038_8090.gene2acc
Eukaryota/UP000001357_81824.fasta
Eukaryota/UP000002149_214684_DNA.miss
Eukaryota/UP000001555_6945.gene2acc
Eukaryota/UP000001038_8090_gcoord.xml
Eukaryota/UP000002149_214684_additional.fasta
Eukaryota/UP000007266_7070.idmapping
Eukaryota/UP000001555_6945.idmapping
Eukaryota/UP000002149_214684.gene2acc
Eukaryota/UP000001555_6945_DNA.fasta
Eukaryota/UP000001357_81824.idmapping
Eukaryota/UP000002149_214684.fasta
Eukaryota/UP000002149_214684.idmapping
Eukaryota/UP000001555_6945.fasta
Eukaryota/UP000000542_5664.gene2acc
Eukaryota/UP000001593_45351.fasta
Eukaryota/UP000008144_7719_DNA.fasta
Eukaryota/UP000001357_81824.gene2acc
Eukaryota/UP000007266_7070_DNA.fasta
Eukaryota/UP000001300_284591_DNA.fasta
Eukaryota/UP000001593_45351.gene2acc
Eukaryota/UP000007266_7070.fasta
Eukaryota/UP000008143_8364.gene2acc
Eukaryota/UP000001555_6945_gcoord.xml
Eukaryota/UP000001300_284591.gene2acc
Eukaryota/UP000001593_45351.idmapping
Eukaryota/UP000008144_7719.fasta
Eukaryota/UP000008144_7719.gene2acc
Eukaryota/UP000008144_7719_additional.fasta
Eukaryota/UP000009136_9913_DNA.fasta
Eukaryota/UP000002280_13616_DNA.fasta
Eukaryota/UP000008144_7719.idmapping
Eukaryota/UP000008143_8364_DNA.miss
Eukaryota/UP000001593_45351_additional.fasta
Eukaryota/UP000001449_35128.idmapping
Eukaryota/UP000008143_8364.idmapping
Eukaryota/UP000008143_8364.fasta
Eukaryota/UP000001300_284591_DNA.miss
Eukaryota/UP000008144_7719_gcoord.xml
Eukaryota/UP000001554_7739.gene2acc
Eukaryota/UP000009136_9913_DNA.miss
Eukaryota/UP000001300_284591.fasta
Eukaryota/UP000009136_9913.fasta
Eukaryota/UP000002280_13616_additional.fasta
Eukaryota/UP000000539_9031_DNA.fasta
Eukaryota/UP000002280_13616.fasta
Eukaryota/UP000000803_7227.idmapping
Eukaryota/UP000002280_13616_DNA.miss
Eukaryota/UP000000803_7227.fasta
Eukaryota/UP000008143_8364_gcoord.xml
Eukaryota/UP000002280_13616.gene2acc
Eukaryota/UP000009136_9913.gene2acc
Eukaryota/UP000002280_13616.idmapping
Eukaryota/UP000001449_35128.fasta
Eukaryota/UP000001449_35128_additional.fasta
Eukaryota/UP000001548_184922.fasta
Eukaryota/UP000001449_35128_DNA.fasta
Eukaryota/UP000002311_559292_DNA.fasta
Eukaryota/UP000001449_35128.gene2acc
Eukaryota/UP000001554_7739_additional.fasta
Eukaryota/UP000002280_13616_gcoord.xml
Eukaryota/UP000009136_9913_additional.fasta
Eukaryota/UP000002311_559292.fasta
Eukaryota/UP000001554_7739_DNA.miss
Eukaryota/UP000009136_9913.idmapping
Eukaryota/UP000000803_7227_DNA.fasta
Eukaryota/UP000000561_237631.fasta
Eukaryota/UP000007305_4577_DNA.miss
Eukaryota/UP000000803_7227.gene2acc
Eukaryota/UP000000539_9031_DNA.miss
Eukaryota/UP000001554_7739_DNA.fasta
Eukaryota/UP000000539_9031.fasta
Eukaryota/UP000009136_9913_gcoord.xml
Eukaryota/UP000002311_559292.gene2acc
Eukaryota/UP000001055_321614.idmapping
Eukaryota/UP000000561_237631.gene2acc
Eukaryota/UP000000561_237631_DNA.fasta
Eukaryota/UP000001055_321614_DNA.fasta
Eukaryota/UP000001554_7739.fasta
Eukaryota/UP000005238_164328.gene2acc
Eukaryota/UP000001554_7739.idmapping
Eukaryota/UP000001055_321614.gene2acc
Eukaryota/UP000002311_559292_DNA.miss
Eukaryota/UP000007241_684364_DNA.fasta
Eukaryota/UP000002311_559292.idmapping
Eukaryota/UP000007241_684364.gene2acc
Eukaryota/UP000000561_237631.idmapping
Eukaryota/UP000007241_684364.fasta
Eukaryota/UP000000539_9031.idmapping
Eukaryota/UP000000539_9031.gene2acc
Eukaryota/UP000002311_559292_gcoord.xml
Eukaryota/UP000000539_9031_additional.fasta
Eukaryota/UP000001548_184922.gene2acc
Eukaryota/UP000007241_684364.idmapping
Eukaryota/UP000001055_321614.fasta
Eukaryota/UP000001548_184922_DNA.fasta
Eukaryota/UP000001542_5722.fasta
Eukaryota/UP000001450_36329.idmapping
Eukaryota/UP000001548_184922.idmapping
Eukaryota/UP000007305_4577_DNA.fasta
Eukaryota/UP000007305_4577.gene2acc
Eukaryota/UP000000539_9031_gcoord.xml
Eukaryota/UP000001940_6239_DNA.miss
Eukaryota/UP000001542_5722_DNA.fasta
Eukaryota/UP000001542_5722.gene2acc
Eukaryota/UP000001542_5722.idmapping
Eukaryota/UP000005238_164328.idmapping
Eukaryota/UP000007305_4577.idmapping
Eukaryota/UP000001940_6239_DNA.fasta
Eukaryota/UP000001940_6239.fasta
Eukaryota/UP000007305_4577.fasta
Eukaryota/UP000000600_5888.fasta
Eukaryota/UP000001940_6239.idmapping
Eukaryota/UP000001940_6239.gene2acc
Eukaryota/UP000005238_164328_DNA.fasta
Eukaryota/UP000001312_665079.idmapping
Eukaryota/UP000018468_7918.idmapping
Eukaryota/UP000005238_164328.fasta
Eukaryota/UP000000589_10090.idmapping
Eukaryota/UP000001450_36329_additional.fasta
Eukaryota/UP000006906_3055_DNA.miss
Eukaryota/UP000001450_36329_DNA.fasta
Eukaryota/UP000000589_10090_DNA.fasta
Eukaryota/UP000001450_36329_DNA.miss
Eukaryota/UP000018468_7918_DNA.fasta
Eukaryota/UP000006906_3055.idmapping
Eukaryota/UP000001450_36329.fasta
Eukaryota/UP000006548_3702.fasta
Eukaryota/UP000001450_36329.gene2acc
Eukaryota/UP000007062_7165_DNA.miss
Eukaryota/UP000007305_4577_gcoord.xml
Eukaryota/UP000018468_7918.gene2acc
Eukaryota/UP000000589_10090_DNA.miss
Eukaryota/UP000000589_10090.fasta
Eukaryota/UP000000589_10090.gene2acc
Eukaryota/UP000005238_164328_gcoord.xml
Eukaryota/UP000000589_10090_additional.fasta
Eukaryota/UP000018468_7918.fasta
Eukaryota/UP000006906_3055_additional.fasta
Eukaryota/UP000006906_3055_DNA.fasta
Eukaryota/UP000006906_3055.gene2acc
Eukaryota/UP000006906_3055.fasta
Eukaryota/UP000000559_237561_additional.fasta
Eukaryota/UP000001519_9595.fasta
Eukaryota/UP000006548_3702_DNA.fasta
Eukaryota/UP000001312_665079_DNA.fasta
Eukaryota/UP000006548_3702_DNA.miss
Eukaryota/UP000002277_9598.idmapping
Eukaryota/UP000000589_10090_gcoord.xml
Eukaryota/UP000006548_3702_additional.fasta
Eukaryota/UP000007062_7165.fasta
Eukaryota/UP000007062_7165.gene2acc
Eukaryota/UP000006548_3702.gene2acc
Eukaryota/UP000006548_3702.idmapping
Eukaryota/UP000018468_7918_gcoord.xml
Eukaryota/UP000001312_665079.fasta
Eukaryota/UP000002485_284812.xml
Eukaryota/UP000001312_665079.gene2acc
Eukaryota/UP000000559_237561.idmapping
Eukaryota/UP000000559_237561_DNA.fasta
Eukaryota/UP000000559_237561_DNA.miss
Eukaryota/UP000000559_237561.fasta
Eukaryota/UP000001548_184922.xml
Eukaryota/UP000000559_237561.gene2acc
Eukaryota/UP000002277_9598.gene2acc
Eukaryota/UP000001519_9595_DNA.fasta
Eukaryota/UP000001300_284591.xml
Eukaryota/UP000006548_3702_gcoord.xml
Eukaryota/UP000002277_9598.fasta
Eukaryota/UP000001519_9595.idmapping
Eukaryota/UP000001519_9595_DNA.miss
Eukaryota/UP000001519_9595.gene2acc
Eukaryota/UP000001519_9595_additional.fasta
Eukaryota/UP000007062_7165.idmapping
Eukaryota/UP000007062_7165_DNA.fasta
Eukaryota/UP000002277_9598_DNA.fasta
Eukaryota/UP000002277_9598_DNA.miss
Eukaryota/UP000002530_330879_DNA.fasta
Eukaryota/UP000015101_6412.xml
Eukaryota/UP000001357_81824.xml
Eukaryota/UP000008144_7719.xml
Eukaryota/UP000002311_559292.xml
Eukaryota/UP000002530_330879.fasta
Eukaryota/UP000002149_214684.xml
Eukaryota/UP000001519_9595_gcoord.xml
Eukaryota/UP000002277_9598_additional.fasta
Eukaryota/UP000000542_5664.xml
Eukaryota/UP000002530_330879.gene2acc
Eukaryota/UP000001449_35128.xml
Eukaryota/UP000002254_9615.xml
Eukaryota/UP000002530_330879.idmapping
Eukaryota/UP000001055_321614.xml
Eukaryota/UP000007062_7165_gcoord.xml
Eukaryota/UP000007266_7070.xml
Eukaryota/UP000006727_3218.xml
Eukaryota/UP000001450_36329.xml
Eukaryota/UP000008783_418459.xml
Eukaryota/UP000000561_237631.xml
Eukaryota/UP000000559_237561.xml
Eukaryota/UP000002277_9598_gcoord.xml
Eukaryota/UP000007241_684364.xml
Eukaryota/UP000001554_7739.xml
Eukaryota/UP000002280_13616.xml
Eukaryota/UP000002530_330879.xml
Eukaryota/UP000000600_5888_DNA.fasta
Eukaryota/UP000000600_5888.gene2acc
Eukaryota/UP000000600_5888.idmapping
Eukaryota/UP000001805_367110_additional.fasta
Eukaryota/UP000001805_367110_DNA.fasta
Eukaryota/UP000001805_367110.idmapping
Eukaryota/UP000001805_367110.gene2acc
Eukaryota/UP000001805_367110.fasta
Eukaryota/UP000005640_9606_DNA.miss
Eukaryota/UP000005640_9606.idmapping
Eukaryota/UP000005640_9606.gene2acc
Eukaryota/UP000002494_10116_additional.fasta
Eukaryota/UP000005640_9606.fasta
Eukaryota/UP000002494_10116.fasta
Eukaryota/UP000002494_10116.gene2acc
Eukaryota/UP000059680_39947_additional.fasta
Eukaryota/UP000002254_9615_additional.fasta
Eukaryota/UP000000437_7955_additional.fasta
Eukaryota/UP000008783_418459_additional.fasta
Eukaryota/UP000007266_7070_additional.fasta
Eukaryota/UP000008143_8364_additional.fasta
Eukaryota/UP000001300_284591_additional.fasta
Eukaryota/UP000000803_7227_additional.fasta
Eukaryota/UP000002311_559292_additional.fasta
Eukaryota/UP000000561_237631_additional.fasta
Eukaryota/UP000001940_6239_additional.fasta
Eukaryota/UP000007305_4577_additional.fasta
Eukaryota/UP000018468_7918_additional.fasta
Eukaryota/UP000007062_7165_additional.fasta
Eukaryota/UP000001805_367110.xml
Eukaryota/UP000005238_164328.xml
Eukaryota/UP000001312_665079.xml
Eukaryota/UP000001593_45351.xml
Eukaryota/UP000001038_8090.xml
Eukaryota/UP000059680_39947.xml
Eukaryota/UP000001555_6945.xml
Eukaryota/UP000000803_7227.xml
Eukaryota/UP000008143_8364.xml
Eukaryota/UP000018468_7918.xml
Eukaryota/UP000009136_9913.xml
Eukaryota/UP000007062_7165.xml
Eukaryota/UP000006906_3055.xml
Eukaryota/UP000000539_9031.xml
Eukaryota/UP000001940_6239.xml
Eukaryota/UP000001542_5722.xml
Eukaryota/UP000001519_9595.xml
Eukaryota/UP000002494_10116.xml
Eukaryota/UP000000437_7955.xml
Eukaryota/UP000000600_5888.xml
Eukaryota/UP000002277_9598.xml
Eukaryota/UP000006548_3702.xml
Eukaryota/UP000000589_10090.xml
Eukaryota/UP000007305_4577.xml
Eukaryota/UP000005640_9606.xml
Eukaryota/UP000002195_44689.xml

# Make protein fasta subfolders_____no_output_____

ls -lhatotal 2.6G
drwxr-xr-x 5 olga root 4.0K Dec 25 18:57 ./
drwxr-xr-x 3 olga root 4.0K Dec 25 17:48 ../
drwxr-xr-x 2 olga czb  4.0K May 10  2019 Archaea/
drwxr-xr-x 2 olga czb   16K May 10  2019 Bacteria/
drwxr-xr-x 2 olga czb   32K May 10  2019 Eukaryota/
-rw-r--r-- 1 olga czb  2.6G Dec 25 18:46 QfO_release_2019_04.tar.gz
-rw-r--r-- 1 olga czb   18K May 10  2019 README
cat README
Universal Protein Resource (UniProt)
====================================

The Universal Protein Resource (UniProt), a collaboration between the European
Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics, and
the Protein Information Resource (PIR), is comprised of three databases, each
optimized for different uses. The UniProt Knowledgebase (UniProtKB) is the
central access point for extensively curated protein information, including
function, classification and cross-references. The UniProt Reference Clusters
(UniRef) combine closely related sequences into a single record to speed up
sequence similarity searches. The UniProt Archive (UniParc) is a comprehensive
repository of all protein sequences, consisting only of unique identifiers and
sequences.

Reference Proteomes QfO release
===============================

Some proteomes have been (manually and algorithmically) selected as reference
proteomes. They cover well-studied model organisms and other organisms of
interest for biomedical research and phylogeny.

Based on UniProt Release 2019_04, Ensembl release 95 and Ensembl Genome
release 42

This folder, ftp.ebi.ac.uk/pub/databases/reference_proteomes/QfO/,
contains the following files, updated once a year:

- README (this file)

- Taxonomic division folders (Archaea, Bacteria and Eukaryota) containing
  *.gene2acc, *.fasta (canonical sequences), *_DNA.fasta, *.xml and *.idmapping
  files for 78 species, plus 41 *_additional.fasta (isoform sequences) and 45
  *_DNA.miss files

- QfO_release_2019_04.tar.gz is an archive that contains all files above.

Release 2019_04, 08-May-2019

Statistics (Total of species = 78):

    #(1) Number of entries in main fasta (canonical)
    #(2) Number of entries in additional fasta (isoforms)
    #(3) Number of entries in gene2acc mapping file

Proteome_ID Tax_ID  OSCODE     #(1)    #(2)    #(3)  Species Name
UP000007062 7165    ANOGA     12553     971   13619  Anopheles gambiae (African malaria mosquito)
UP000000798 224324  AQUAE      1553       0    1557  Aquifex aeolicus (strain VF5)
UP000006548 3702    ARATH     27475   14123   41920  Arabidopsis thaliana (Mouse-ear cress)
UP000001570 224308  BACSU      4260       7    4268  Bacillus subtilis (strain 168)
UP000001414 226186  BACTN      4782       0    4823  Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
UP000007241 684364  BATDJ      8610       0    8685  Batrachochytrium dendrobatidis (strain JAM81 / FGSC 10211) (Frog chytrid fungus)
UP000009136 9913    BOVIN     23774   14534   38438  Bos taurus (Bovine)
UP000002526 224911  BRADU      8253       0    8314  Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
UP000001554 7739    BRAFL     28542       2   28608  Branchiostoma floridae (Florida lancelet) (Amphioxus)
UP000001940 6239    CAEEL     19986    8309   28507  Caenorhabditis elegans
UP000000559 237561  CANAL      6035       1    6051  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)
UP000002254 9615    CANLF     20271    5269   25631  Canis lupus familiaris (Dog) (Canis familiaris)
UP000000431 272561  CHLTR       895       0     895  Chlamydia trachomatis (strain D/UW-3/Cx)
UP000006906 3055    CHLRE     17614    1214   19033  Chlamydomonas reinhardtii (Chlamydomonas smithii)
UP000002008 324602  CHLAA      3850       0    3853  Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)
UP000008144 7719    CIOIN     16678     631   17317  Ciona intestinalis (Transparent sea squirt) (Ascidia intestinalis)
UP000002149 214684  CRYNJ      6604     142    6773  Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) (Filobasidiella neoformans)
UP000000437 7955    DANRE     25939   21219   47517  Danio rerio (Zebrafish) (Brachydanio rerio)
UP000002524 243230  DEIRA      3085       0    3103  Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
UP000007719 515635  DICTD      1743       0    1744  Dictyoglomus turgidum (strain Z-1310 / DSM 6724)
UP000002195 44689   DICDI     12739      27   13120  Dictyostelium discoideum (Slime mold)
UP000000803 7227    DROME     13788    9516   23457  Drosophila melanogaster (Fruit fly)
UP000000625 83333   ECOLI      4391      12    8529  Escherichia coli (strain K12)
UP000002521 190304  FUSNN      2046       0    2064  Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131)
UP000000539 9031    CHICK     18124    9932   28206  Gallus gallus (Chicken)
UP000000577 243231  GEOSL      3402       0    3433  Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)
UP000001548 184922  GIAIC      7154       0    7364  Giardia intestinalis (strain ATCC 50803 / WB clone C6) (Giardia lamblia)
UP000000557 251221  GLOVI      4406       0    4427  Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)
UP000001519 9595    GORGO     21795   22932   44943  Gorilla gorilla gorilla (Western lowland gorilla)
UP000000554 64091   HALSA      2426       0    2607  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halobacterium halobium)
UP000000429 85962   HELPY      1553       0    1577  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
UP000015101 6412    HELRO     23328       0   23433  Helobdella robusta (Californian leech)
UP000005640 9606    HUMAN     21146   74769   96332  Homo sapiens (Human)
UP000001555 6945    IXOSC     20473       0   20482  Ixodes scapularis (Black-legged tick) (Deer tick)
UP000001686 374847  KORCO      1602       0    1602  Korarchaeum cryptofilum (strain OPF8)
UP000000542 5664    LEIMA      8038       0    8315  Leishmania major
UP000018468 7918    LEPOC     18320    4140   22480  Lepisosteus oculatus (Spotted gar)
UP000001408 189518  LEPIN      3676       0    3707  Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
UP000000805 243232  METJA      1787       0    1788  Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
UP000002487 188937  METAC      4468       0    4540  Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)
UP000002280 13616   MONDO     21276     968   22319  Monodelphis domestica (Gray short-tailed opossum)
UP000001357 81824   MONBE      9188       0    9204  Monosiga brevicollis (Choanoflagellate)
UP000000589 10090   MOUSE     22287   40369   63134  Mus musculus (Mouse)
UP000001584 83332   MYCTU      3993       4    5634  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
UP000000807 243273  MYCGE       483       0     483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)
UP000000425 122586  NEIMB      2001       0    2062  Neisseria meningitidis serogroup B (strain MC58)
UP000001593 45351   NEMVE     24429      15   24622  Nematostella vectensis (Starlet sea anemone)
UP000002530 330879  ASPFU      9647       0    9652  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (Aspergillus fumigatus)
UP000001805 367110  NEUCR      9759     508   10271  Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
UP000000792 436308  NITMS      1795       0    1795  Nitrosopumilus maritimus (strain SCM1)
UP000059680 39947   ORYSJ     43858    5369   51020  Oryza sativa subsp. japonica (Rice)
UP000001038 8090    ORYLA     23617   12536   36234  Oryzias latipes (Japanese rice fish) (Japanese killifish)
UP000002277 9598    PANTR     23006   25788   49266  Pan troglodytes (Chimpanzee)
UP000000600 5888    PARTE     39461       0   39753  Paramecium tetraurelia
UP000001055 321614  PHANO     15998       0   16008  Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) (Glume blotch fungus) (Parastagonospora nodorum)
UP000006727 3218    PHYPA     30792      66   31878  Physcomitrella patens subsp. patens (Moss)
UP000005238 164328  PHYRM     15349       0   15605  Phytophthora ramorum (Sudden oak death agent)
UP000001450 36329   PLAF7      5448       1    5463  Plasmodium falciparum (isolate 3D7)
UP000002438 208964  PSEAE      5563       2    5576  Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
UP000008783 418459  PUCGT     15689     119   15920  Puccinia graminis f. sp. tritici (strain CRL 75-36-700-3 / race SCCL) (Black stem rust fungus)
UP000002494 10116   RAT       21678    9885   32629  Rattus norvegicus (Rat)
UP000001025 243090  RHOBA      7271       0    7325  Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)
UP000001974 273057  SACS2      2938       0    2995  Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (Sulfolobus solfataricus)
UP000002311 559292  YEAST      6049      28    6082  Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
UP000002485 284812  SCHPO      5141       9    5154  Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
UP000001312 665079  SCLS1     14445       0   14472  Sclerotinia sclerotiorum (strain ATCC 18683 / 1980 / Ss-1) (White mold) (Whetzelinia sclerotiorum)
UP000001973 100226  STRCO      8038       1    8154  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
UP000001425 1111708 SYNY3      3507       0    3565  Synechocystis sp. (strain PCC 6803 / Kazusa)
UP000001449 35128   THAPS     11717       1   11762  Thalassiosira pseudonana (Marine diatom) (Cyclotella nana)
UP000000536 69014   THEKO      2301       0    2305  Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
UP000000718 289376  THEYD      1982       0    2033  Thermodesulfovibrio yellowstonii (strain ATCC 51303 / DSM 11347 / YP87)
UP000008183 243274  THEMA      1852       0    2872  Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
UP000007266 7070    TRICA     16579    1926   18539  Tribolium castaneum (Red flour beetle)
UP000001542 5722    TRIVA     50190       0   59533  Trichomonas vaginalis
UP000000561 237631  USTMA      6788      18    6809  Ustilago maydis (strain 521 / FGSC 9021) (Corn smut fungus)
UP000008143 8364    XENTR     24386    5307   29884  Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
UP000001300 284591  YARLI      6449       5    6477  Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
UP000007305 4577    MAIZE     39448   59948  100330  Zea mays (Maize)

Gene mapping files (*.gene2acc)
===============================

Column 1 is a unique gene symbol that is chosen with the following order of
preference from the annotation found in:
1) Model Organism Database (MOD)
2) Ensembl or Ensembl Genomes database
3) UniProt Ordered Locus Name (OLN)
4) UniProt Open Reading Frame (ORF)
5) UniProt Gene Name
A dash symbol ('-') is used when the gene encoding a protein is unknown.

Column 2 is the UniProtKB accession or isoform identifier for the given gene
symbol. This column may have redundancy when two or more genes have identical
translations.

Column 3 is the gene symbol of the canonical accession used to represent the
respective gene group and the first row of the sequence is the canonical one.

Protein FASTA files (*.fasta and *_additional.fasta)
====================================================

These files, composed of canonical and additional sequences, are non-redundant
FASTA sets for the sequences of each reference proteome.
The additional set contains isoform/variant sequences for a given gene, and its
FASTA header indicates the corresponding canonical sequence ("Isoform of ...").
The FASTA format is the standard UniProtKB format.

For further references about the standard UniProtKB format, please see:
    http://www.uniprot.org/help/fasta-headers
    http://www.uniprot.org/faq/38

E.g. Canonical set:
>sp|Q9H6Y5|MAGIX_HUMAN PDZ domain-containing protein MAGIX OS=Homo sapiens GN=MAGIX PE=1 SV=3
MEPRTGGAANPKGSRGSRGPSPLAGPSARQLLARLDARPLAARAAVDVAALVRRAGATLR
LRRKEAVSVLDSADIEVTDSRLPHATIVDHRPQHRWLETCNAPPQLIQGKAHSAPKPSQA
SGHFSVELVRGYAGFGLTLGGGRDVAGDTPLAVRGLLKDGPAQRCGRLEVGDVVLHINGE
STQGLTHAQAVERIRAGGPQLHLVIRRPLETHPGKPRGVGEPRKGVVPSWPDRSPDPGGP
EVTGSRSSSTSLVQHPPSRTTLKKTRGSPEPSPEAAADGPTVSPPERRAEDPNDQIPGSP
GPWLVPSEERLSRALGVRGAAQFAQEMAAGRRRH

E.g. Additional sets:
>sp|Q9H6Y5-2|MAGIX_HUMAN Isoform of Q9H6Y5, Isoform 2 of PDZ domain-containing protein MAGIX OS=Homo sapiens GN=MAGIX
MPLLWITGPRYHLILLSEASCLRANYVHLCPLFQHRWLETCNAPPQLIQGKAHSAPKPSQ
ASGHFSVELVRGYAGFGLTLGGGRDVAGDTPLAVRGLLKDGPAQRCGRLEVGDVVLHING
ESTQGLTHAQAVERIRAGGPQLHLVIRRPLETHPGKPRGVGEPRKGVVPSWPDRSPDPGG
PEVTGSRSSSTSLVQHPPSRTTLKKTRGSPEPSPEAAADGPTVSPPERRAEDPNDQIPGS
PGPWLVPSEERLSRALGVRGAAQFAQEMAAGRRRH
>tr|C9J123|C9J123_HUMAN Isoform of Q9H6Y5, PDZ domain-containing protein MAGIX (Fragment) OS=Homo sapiens GN=MAGIX PE=1 SV=2
MSPNSPLHCFYLPAVSVLDSADIEVTDSRLPHATIVDHRPQVGDLVLHINGESTQGLTHA
QAVERIRAGGPQLHLVIRRPLETHPGKPRGVGEPRKGVDRSPDPGGPEVTGSRSSSTSLV
QHPPSRTTLKKTRGSPEPSPEAA

Coding DNA Sequence FASTA files (*_DNA.fasta)
=============================================

These files contain the coding DNA sequences (CDS) for the protein sequences
where it was possible.
The format is as in the following example (UP000005640_9606_DNA.fasta):

>sp|A0A183|ENSP00000411070
ATGTCACAGCAGAAGCAGCAATCTTGGAAGCCTCCAAATGTTCCCAAATGCTCCCCTCCC
CAAAGATCAAACCCCTGCCTAGCTCCCTACTCGACTCCTTGTGGTGCTCCCCATTCAGAA
GGTTGTCATTCCAGTTCCCAAAGGCCTGAGGTTCAGAAGCCTAGGAGGGCTCGTCAAAAG
CTGCGCTGCCTAAGTAGGGGCACAACCTACCACTGCAAAGAGGAAGAGTGTGAAGGCGAC
TGA

The 3 fields of the FASTA header are:
1) 'sp' (Swiss-Prot reviewed) or 'tr' (TrEMBL)
2) UniProtKB Accession
3) EMBL Protein ID or Ensembl/Ensembl Genome ID

Unsuccessful Coding DNA Sequence mapping files (*_DNA.miss)
===========================================================

For the species that did not have a perfect mapping for all protein sequences
to a CDS, these files contain the entries that could not be mapped.
The format is as in the following example (UP000005640_9606_DNA.miss):

sp      A6NF01  CAUTION: Could be the product of a pseudogene.
sp      A6NFI3  NOT_ANNOTATED_CDS

The 3 fields are:
1) 'sp' (Swiss-Prot reviewed) or 'tr' (TrEMBL)
2) UniProtKB accession
3) Reason why the protein could not be mapped to a CDS

Database mapping files (*.idmapping)
====================================

These files contain mappings from UniProtKB to other databases for each
reference proteome.
The format consists of three tab-separated columns:

1. UniProtKB accession
2. ID_type:
   Database name as shown in UniProtKB cross-references and supported by the ID
   mapping tool on the UniProt web site (http://www.uniprot.org/mapping)
3. ID:
   Identifier in the cross-referenced database.

SeqXML files (*.xml)
====================

The xml files contain all the information from fasta (canonical and additional),
idmapping and CDS in SeqXML format (see http://seqxml.org.)
E.g. (from UP000005640_9606.xml, header and one entry)

<?xml version="1.0" encoding="utf-8"?>
<seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" speciesName="Homo sapiens" xsi:noNamespaceSchemaLocation="http://www.seqxml.org/0.4/seqxml.xsd" seqXMLversion="0.4" sourceVersion="2016_04" source="QfO http://w
ww.ebi.ac.uk/reference_proteomes/" ncbiTaxID="9606">
  <entry source="UniProtKB" id="U3KQE9">
    <description>Uncharacterized protein (Fragment)</description>
    <AAseq>XLLLAINGVTECFTFAAMSKEEVDRYNFVMLALSSSFLVLSYLLTRWCGSVGFILANCFNMGIRITQSLCFIHRYYRRSPHRPLAGLHLSPVLLGTFALSGGVTAVSERPRKPWRSSGPWCPC</AAseq>
    <DBRef source="UniProtKB-ID" id="U3KQE9_HUMAN"/>
    <DBRef source="UniRef100" id="UniRef100_U3KQE9"/>
    <DBRef source="UniRef90" id="UniRef90_U3KQE9"/>
    <DBRef source="UniRef50" id="UniRef50_U3KQE9"/>
    <DBRef source="UniParc" id="UPI00038BAF87"/>
    <DBRef source="EMBL" id="AC096887"/>
    <DBRef source="EMBL" id="AC099667"/>
    <DBRef source="EMBL" id="AC103589"/>
    <DBRef source="EMBL-CDS" id="-"/>
    <DBRef source="NCBI_TaxID" id="9606"/>
    <DBRef source="STRING" id="9606.ENSP00000296292"/>
    <DBRef source="Ensembl" id="ENSG00000272305"/>
    <DBRef source="Ensembl_TRS" id="ENST00000607283"/>
    <DBRef source="Ensembl_PRO" id="ENSP00000475819"/>
    <DBRef source="UCSC" id="uc062krn.1"/>
    <DBRef source="eggNOG" id="KOG2864"/>
    <DBRef source="eggNOG" id="ENOG410Y1D5"/>
    <DBRef source="GeneTree" id="ENSGT00390000011390"/>
    <DBRef source="OMA" id="ERPRKPW"/>
    <DBRef source="UniProt" id="U3KQG8"/>
    <DBRef source="UniProt" id="U3KQK6"/>
    <property name="DNAsource" value="ENSP00000475819"/>
    <property name="ensemblVersion" value="84,31"/>
    <property name="UPID" value="UP000005640"/>
    <property name="SV" value="1"/>
    <property name="DNAseq" value="NTTCTCCTGCTTGCCATCAATGGAGTGACAGAGTGTTTCACATTTGCTGCCATGAGCAAAGAGGAGGTCGACAGGTACAATTTTGTGATGCTGGCCCTGTCCTCCTCATTCCTGGTGTTATCCTATCTCTTGACCCGTTGGTGTGGCAGCGTGGGCTTCATCTTGGCCAACTGCTTTAACATGGGCATTCGGATCACGCAGAGCCTTTGCTTCATCCACCGCTACTACCGAAGGAGCCCCCACAGGCCCCTGGCTGGCCTGCACCTATCGCCAGTCCTGCTCGGGACATTTGCCCTCAGTGGTGGGGTTACTGCTGTTTCGGAGAGGCCAAGAAAACCATGGAGGAGCAGTGGACCTTGGTGTCCCTGCTGA"/>
    <property name="PE" value="4"/>
  </entry>

--------------------------------------------------------------------------------
  LICENSE
--------------------------------------------------------------------------------
We have chosen to apply the Creative Commons Attribution (CC BY 4.0) License
(https://creativecommons.org/licenses/by/4.0/) to all copyrightable parts of
our databases.

(c) 2002-2019 UniProt Consortium

--------------------------------------------------------------------------------
  DISCLAIMER
--------------------------------------------------------------------------------
We make no warranties regarding the correctness of the data, and disclaim
liability for damages resulting from its use. We cannot provide unrestricted
permission regarding the use of the data, as some data may be covered by patents
or other rights.

Any medical or genetic information is provided for research, educational and
informational purposes only. It is not in any way intended to be used as a
substitute for professional medical advice, diagnosis, treatment or care.
%%bash

for DIR in $(ls -F | grep '/'); do
    cd $DIR
#     rm -rf protein-fastas
    mkdir protein-fastas
    # xargs ftw!!
    ls -1 *.fasta | grep -v DNA | xargs -I{} ln -s $PWD/{} protein-fastas/{}
    cd ..
done_____no_output_____ls -lha Eukaryota/protein-fastastotal 82K
drwxr-xr-x 2 olga czb 8.0K Dec 25 19:08 ./
drwxr-xr-x 3 olga czb  32K Dec 25 19:08 ../
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000000437_7955_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000437_7955_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000000437_7955.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000437_7955.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000000539_9031_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000539_9031_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000000539_9031.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000539_9031.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000000542_5664.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000542_5664.fasta
lrwxrwxrwx 1 olga czb  106 Dec 25 19:08 UP000000559_237561_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000559_237561_additional.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000000559_237561.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000559_237561.fasta
lrwxrwxrwx 1 olga czb  106 Dec 25 19:08 UP000000561_237631_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000561_237631_additional.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000000561_237631.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000561_237631.fasta
lrwxrwxrwx 1 olga czb  105 Dec 25 19:08 UP000000589_10090_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000589_10090_additional.fasta
lrwxrwxrwx 1 olga czb   94 Dec 25 19:08 UP000000589_10090.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000589_10090.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000000600_5888.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000600_5888.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000000803_7227_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000803_7227_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000000803_7227.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000803_7227.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000001038_8090_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001038_8090_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000001038_8090.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001038_8090.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000001055_321614.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001055_321614.fasta
lrwxrwxrwx 1 olga czb  106 Dec 25 19:08 UP000001300_284591_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001300_284591_additional.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000001300_284591.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001300_284591.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000001312_665079.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001312_665079.fasta
lrwxrwxrwx 1 olga czb   94 Dec 25 19:08 UP000001357_81824.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001357_81824.fasta
lrwxrwxrwx 1 olga czb  105 Dec 25 19:08 UP000001449_35128_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001449_35128_additional.fasta
lrwxrwxrwx 1 olga czb   94 Dec 25 19:08 UP000001449_35128.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001449_35128.fasta
lrwxrwxrwx 1 olga czb  105 Dec 25 19:08 UP000001450_36329_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001450_36329_additional.fasta
lrwxrwxrwx 1 olga czb   94 Dec 25 19:08 UP000001450_36329.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001450_36329.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000001519_9595_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001519_9595_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000001519_9595.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001519_9595.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000001542_5722.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001542_5722.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000001548_184922.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001548_184922.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000001554_7739_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001554_7739_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000001554_7739.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001554_7739.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000001555_6945.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001555_6945.fasta
lrwxrwxrwx 1 olga czb  105 Dec 25 19:08 UP000001593_45351_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001593_45351_additional.fasta
lrwxrwxrwx 1 olga czb   94 Dec 25 19:08 UP000001593_45351.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001593_45351.fasta
lrwxrwxrwx 1 olga czb  106 Dec 25 19:08 UP000001805_367110_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001805_367110_additional.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000001805_367110.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001805_367110.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000001940_6239_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001940_6239_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000001940_6239.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000001940_6239.fasta
lrwxrwxrwx 1 olga czb  106 Dec 25 19:08 UP000002149_214684_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002149_214684_additional.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000002149_214684.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002149_214684.fasta
lrwxrwxrwx 1 olga czb  105 Dec 25 19:08 UP000002195_44689_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002195_44689_additional.fasta
lrwxrwxrwx 1 olga czb   94 Dec 25 19:08 UP000002195_44689.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002195_44689.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000002254_9615_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002254_9615_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000002254_9615.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002254_9615.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000002277_9598_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002277_9598_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000002277_9598.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002277_9598.fasta
lrwxrwxrwx 1 olga czb  105 Dec 25 19:08 UP000002280_13616_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002280_13616_additional.fasta
lrwxrwxrwx 1 olga czb   94 Dec 25 19:08 UP000002280_13616.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002280_13616.fasta
lrwxrwxrwx 1 olga czb  106 Dec 25 19:08 UP000002311_559292_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002311_559292_additional.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000002311_559292.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002311_559292.fasta
lrwxrwxrwx 1 olga czb  106 Dec 25 19:08 UP000002485_284812_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002485_284812_additional.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000002485_284812.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002485_284812.fasta
lrwxrwxrwx 1 olga czb  105 Dec 25 19:08 UP000002494_10116_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002494_10116_additional.fasta
lrwxrwxrwx 1 olga czb   94 Dec 25 19:08 UP000002494_10116.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002494_10116.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000002530_330879.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000002530_330879.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000005238_164328.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000005238_164328.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000005640_9606_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000005640_9606_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000005640_9606.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000005640_9606.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000006548_3702_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000006548_3702_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000006548_3702.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000006548_3702.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000006727_3218_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000006727_3218_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000006727_3218.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000006727_3218.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000006906_3055_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000006906_3055_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000006906_3055.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000006906_3055.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000007062_7165_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000007062_7165_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000007062_7165.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000007062_7165.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000007241_684364.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000007241_684364.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000007266_7070_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000007266_7070_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000007266_7070.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000007266_7070.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000007305_4577_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000007305_4577_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000007305_4577.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000007305_4577.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000008143_8364_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000008143_8364_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000008143_8364.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000008143_8364.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000008144_7719_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000008144_7719_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000008144_7719.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000008144_7719.fasta
lrwxrwxrwx 1 olga czb  106 Dec 25 19:08 UP000008783_418459_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000008783_418459_additional.fasta
lrwxrwxrwx 1 olga czb   95 Dec 25 19:08 UP000008783_418459.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000008783_418459.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000009136_9913_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000009136_9913_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000009136_9913.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000009136_9913.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000015101_6412.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000015101_6412.fasta
lrwxrwxrwx 1 olga czb  104 Dec 25 19:08 UP000018468_7918_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000018468_7918_additional.fasta
lrwxrwxrwx 1 olga czb   93 Dec 25 19:08 UP000018468_7918.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000018468_7918.fasta
lrwxrwxrwx 1 olga czb  105 Dec 25 19:08 UP000059680_39947_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000059680_39947_additional.fasta
lrwxrwxrwx 1 olga czb   94 Dec 25 19:08 UP000059680_39947.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000059680_39947.fasta

# How many total Eukaryotic protein sequences are there?_____no_output_____

! grep --count '>' Eukaryota/protein-fastas/* Eukaryota/protein-fastas/UP000000437_7955.fasta:25939
Eukaryota/protein-fastas/UP000000437_7955_additional.fasta:21219
Eukaryota/protein-fastas/UP000000539_9031.fasta:18124
Eukaryota/protein-fastas/UP000000539_9031_additional.fasta:9932
Eukaryota/protein-fastas/UP000000542_5664.fasta:8038
Eukaryota/protein-fastas/UP000000559_237561.fasta:6035
Eukaryota/protein-fastas/UP000000559_237561_additional.fasta:1
Eukaryota/protein-fastas/UP000000561_237631.fasta:6788
Eukaryota/protein-fastas/UP000000561_237631_additional.fasta:18
Eukaryota/protein-fastas/UP000000589_10090.fasta:22287
Eukaryota/protein-fastas/UP000000589_10090_additional.fasta:40369
Eukaryota/protein-fastas/UP000000600_5888.fasta:39461
Eukaryota/protein-fastas/UP000000803_7227.fasta:13788
Eukaryota/protein-fastas/UP000000803_7227_additional.fasta:9516
Eukaryota/protein-fastas/UP000001038_8090.fasta:23617
Eukaryota/protein-fastas/UP000001038_8090_additional.fasta:12536
Eukaryota/protein-fastas/UP000001055_321614.fasta:15998
Eukaryota/protein-fastas/UP000001300_284591.fasta:6449
Eukaryota/protein-fastas/UP000001300_284591_additional.fasta:5
Eukaryota/protein-fastas/UP000001312_665079.fasta:14445
Eukaryota/protein-fastas/UP000001357_81824.fasta:9188
Eukaryota/protein-fastas/UP000001449_35128.fasta:11717
Eukaryota/protein-fastas/UP000001449_35128_additional.fasta:1
Eukaryota/protein-fastas/UP000001450_36329.fasta:5448
Eukaryota/protein-fastas/UP000001450_36329_additional.fasta:1
Eukaryota/protein-fastas/UP000001519_9595.fasta:21795
Eukaryota/protein-fastas/UP000001519_9595_additional.fasta:22932
Eukaryota/protein-fastas/UP000001542_5722.fasta:50190
Eukaryota/protein-fastas/UP000001548_184922.fasta:7154
Eukaryota/protein-fastas/UP000001554_7739.fasta:28542
Eukaryota/protein-fastas/UP000001554_7739_additional.fasta:2
Eukaryota/protein-fastas/UP000001555_6945.fasta:20473
Eukaryota/protein-fastas/UP000001593_45351.fasta:24429
Eukaryota/protein-fastas/UP000001593_45351_additional.fasta:15
Eukaryota/protein-fastas/UP000001805_367110.fasta:9759
Eukaryota/protein-fastas/UP000001805_367110_additional.fasta:508
Eukaryota/protein-fastas/UP000001940_6239.fasta:19986
Eukaryota/protein-fastas/UP000001940_6239_additional.fasta:8309
Eukaryota/protein-fastas/UP000002149_214684.fasta:6604
Eukaryota/protein-fastas/UP000002149_214684_additional.fasta:142
Eukaryota/protein-fastas/UP000002195_44689.fasta:12739
Eukaryota/protein-fastas/UP000002195_44689_additional.fasta:27
Eukaryota/protein-fastas/UP000002254_9615.fasta:20271
Eukaryota/protein-fastas/UP000002254_9615_additional.fasta:5269
Eukaryota/protein-fastas/UP000002277_9598.fasta:23006
Eukaryota/protein-fastas/UP000002277_9598_additional.fasta:25788
Eukaryota/protein-fastas/UP000002280_13616.fasta:21276
Eukaryota/protein-fastas/UP000002280_13616_additional.fasta:968
Eukaryota/protein-fastas/UP000002311_559292.fasta:6049
Eukaryota/protein-fastas/UP000002311_559292_additional.fasta:28
Eukaryota/protein-fastas/UP000002485_284812.fasta:5141
Eukaryota/protein-fastas/UP000002485_284812_additional.fasta:9
Eukaryota/protein-fastas/UP000002494_10116.fasta:21678
Eukaryota/protein-fastas/UP000002494_10116_additional.fasta:9885
Eukaryota/protein-fastas/UP000002530_330879.fasta:9647
Eukaryota/protein-fastas/UP000005238_164328.fasta:15349
Eukaryota/protein-fastas/UP000005640_9606.fasta:20874
Eukaryota/protein-fastas/UP000005640_9606_additional.fasta:75041
Eukaryota/protein-fastas/UP000006548_3702.fasta:27475
Eukaryota/protein-fastas/UP000006548_3702_additional.fasta:14123
Eukaryota/protein-fastas/UP000006727_3218.fasta:30792
Eukaryota/protein-fastas/UP000006727_3218_additional.fasta:66
Eukaryota/protein-fastas/UP000006906_3055.fasta:17614
Eukaryota/protein-fastas/UP000006906_3055_additional.fasta:1214
Eukaryota/protein-fastas/UP000007062_7165.fasta:12553
Eukaryota/protein-fastas/UP000007062_7165_additional.fasta:971
Eukaryota/protein-fastas/UP000007241_684364.fasta:8610
Eukaryota/protein-fastas/UP000007266_7070.fasta:16579
Eukaryota/protein-fastas/UP000007266_7070_additional.fasta:1926
Eukaryota/protein-fastas/UP000007305_4577.fasta:39448
Eukaryota/protein-fastas/UP000007305_4577_additional.fasta:59948
Eukaryota/protein-fastas/UP000008143_8364.fasta:24386
Eukaryota/protein-fastas/UP000008143_8364_additional.fasta:5307
Eukaryota/protein-fastas/UP000008144_7719.fasta:16678
Eukaryota/protein-fastas/UP000008144_7719_additional.fasta:631
Eukaryota/protein-fastas/UP000008783_418459.fasta:15689
Eukaryota/protein-fastas/UP000008783_418459_additional.fasta:119
Eukaryota/protein-fastas/UP000009136_9913.fasta:23774
Eukaryota/protein-fastas/UP000009136_9913_additional.fasta:14534
Eukaryota/protein-fastas/UP000015101_6412.fasta:23328
Eukaryota/protein-fastas/UP000018468_7918.fasta:18320
Eukaryota/protein-fastas/UP000018468_7918_additional.fasta:4140
Eukaryota/protein-fastas/UP000059680_39947.fasta:43858
Eukaryota/protein-fastas/UP000059680_39947_additional.fasta:5369
! grep  '>' Eukaryota/protein-fastas/* | wc -l1242257
n = 1242257
n_comparisons = int((n * (n - 1))/2)
f'{n:,} sequences --> {n_comparisons:,} comparisons'_____no_output_____

6 milliseconds per comparison_____no_output_____

n_alphabets = 8_____no_output_____n_seconds_per_comparison = 0.0006_____no_output_____(n_comparisons * n_seconds_per_comparison)/60/60_____no_output_____ksize_min = 3
ksize_max = 45_____no_output_____n_ksizes = ksize_max - ksize_min + 1
n_ksizes_____no_output_____n_ksizes * n_alphabets * n_comparisons * 6e-6_____no_output_____human_id = 'UP000005640'
! grep --count '>' Eukaryota/protein-fastas/$human_id* Eukaryota/protein-fastas/UP000005640_9606.fasta:20874
Eukaryota/protein-fastas/UP000005640_9606_additional.fasta:75041
! grep '>' Eukaryota/protein-fastas/$human_id* | wc -l95915
n_human_seqs = 95915
f'{n_human_seqs:,}'_____no_output_____n_not_human_seqs = n - n_human_seqs
n_not_human_seqs_____no_output_____n_human_seqs * n_not_human_seqs_____no_output_____f'{n_human_seqs * n_not_human_seqs:,}'_____no_output_____(n_human_seqs * n_not_human_seqs) * n_seconds_per_comparison_____no_output_____(n_human_seqs * n_not_human_seqs) * n_seconds_per_comparison /60/60_____no_output_____(n_human_seqs * n_not_human_seqs) * n_seconds_per_comparison /60/60/120_____no_output_____(n_human_seqs * n_not_human_seqs) * n_seconds_per_comparison /60/60/120/24_____no_output_____(n_human_seqs * n_not_human_seqs) * n_seconds_per_comparison/2/60/60/120/24_____no_output_____n_human_seqs * n_seconds_per_comparison_____no_output_____n_not_human_seqs * n_seconds_per_comparison_____no_output_____n_not_human_seqs * n_seconds_per_comparison / 60_____no_output_____

## Make separate folders for human and non-human_____no_output_____

%%bash

HUMAN=UP000005640

for DIR in $(ls -F | grep '/'); do
    cd $DIR
#     rm -rf protein-fastas
    mkdir human-protein-fastas
    mkdir not-human-protein-fastas
    # xargs ftw!!
    ls -1 *.fasta | grep -v DNA | grep $HUMAN | xargs -I{} ln -s $PWD/{} human-protein-fastas/{}
    ls -1 *.fasta | grep -v DNA | grep -v $HUMAN | xargs -I{} ln -s $PWD/{} not-human-protein-fastas/{}
    cd ..
done_____no_output_____ll Eukaryota/| headtotal 15484342
drwxr-xr-x 2 olga       4096 Dec 26 19:44 human-protein-fastas/
drwxr-xr-x 2 olga       8192 Dec 26 19:44 not-human-protein-fastas/
drwxr-xr-x 2 olga       8192 Dec 25 19:08 protein-fastas/
-rw-r--r-- 1 olga   13705795 Apr 11  2019 UP000000437_7955_additional.fasta
-rw-r--r-- 1 olga   43123842 Apr 13  2019 UP000000437_7955_DNA.fasta
-rw-r--r-- 1 olga       2634 Apr 13  2019 UP000000437_7955_DNA.miss
-rw-r--r-- 1 olga   16760669 Apr 11  2019 UP000000437_7955.fasta
-rw-r--r-- 1 olga  405525201 May  6  2019 UP000000437_7955_gcoord.xml
-rw-r--r-- 1 olga    2598262 Apr 11  2019 UP000000437_7955.gene2acc
ls: write error
ll Eukaryota/human-protein-fastas | headtotal 1
lrwxrwxrwx 1 olga 104 Dec 26 19:44 UP000005640_9606_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000005640_9606_additional.fasta
lrwxrwxrwx 1 olga  93 Dec 26 19:44 UP000005640_9606.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000005640_9606.fasta
ls -1 Eukaryota/human-protein-fastas | wc -l2
ll Eukaryota/not-human-protein-fastas | headtotal 41
lrwxrwxrwx 1 olga 104 Dec 26 19:44 UP000000437_7955_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000437_7955_additional.fasta
lrwxrwxrwx 1 olga  93 Dec 26 19:44 UP000000437_7955.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000437_7955.fasta
lrwxrwxrwx 1 olga 104 Dec 26 19:44 UP000000539_9031_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000539_9031_additional.fasta
lrwxrwxrwx 1 olga  93 Dec 26 19:44 UP000000539_9031.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000539_9031.fasta
lrwxrwxrwx 1 olga  93 Dec 26 19:44 UP000000542_5664.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000542_5664.fasta
lrwxrwxrwx 1 olga 106 Dec 26 19:44 UP000000559_237561_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000559_237561_additional.fasta
lrwxrwxrwx 1 olga  95 Dec 26 19:44 UP000000559_237561.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000559_237561.fasta
lrwxrwxrwx 1 olga 106 Dec 26 19:44 UP000000561_237631_additional.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000561_237631_additional.fasta
lrwxrwxrwx 1 olga  95 Dec 26 19:44 UP000000561_237631.fasta -> /mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/UP000000561_237631.fasta
ls: write error
ls -1 Eukaryota/not-human-protein-fastas | wc -l82
ls -1 Eukaryota/protein-fastas | wc -l84

## Concatenate human sequences into one file_____no_output_____

mkdir Eukaryota/human-protein-fastas-concatenated/_____no_output_____cat Eukaryota/human-protein-fastas/* > Eukaryota/human-protein-fastas-concatenated/$human_id\.fasta_____no_output_____ll $PWD/Eukaryota/human-protein-fastas-concatenated/total 49472
-rw-r--r-- 1 olga 50656898 Dec 26 19:49 UP000005640.fasta
!echo $PWD/Eukaryota/human-protein-fastas-concatenated/UP000005640.fasta/mnt/data_sm/olga/kmer-hashing/quest-for-orthologs/data/2019/Eukaryota/human-protein-fastas-concatenated/UP000005640.fasta


# Notebook from inferential/BIO-BTE-06-L-7
Path: Notebooks/NB05a_Quantification.ipynb

# NB05a Quantification

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/CSBiology/BIO-BTE-06-L-7/gh-pages?filepath=NB05a_Quantification.ipynb)

[Download Notebook](https://github.com/CSBiology/BIO-BTE-06-L-7/releases/download/NB05a/NB05a_Quantification.ipynb)

1. Quantification Theory
    1. Targeted quantification
    2. (i) Targeted acquisition at peptide
    3. (ii) Targeted data analysis at peptide ion level
2. References

## Quantification Theory

To estimate the amount of individual proteins in complex mixtures, all peptide signals corresponding to a common protein serve as a
proxy for their abundance. Peptide information needs to be obtained from multidimensional signal data detected by the mass spectrometer.
All signals generated from one peptide ion species, often referred to as peptide feature, need to be grouped to form a three-dimensional peak
along the m/z, ion intensity, and retention time dimension. This process is generally defined as peak detection or feature detection.
Peak detection algorithms are a set of rules defining how neighboring signal points are joined. Whether noise filtering is done before or after
peak detection strongly depends on the peak detection algorithm. Traditional approaches mainly focused on signal amplitude neglecting
characteristic peak shapes as a common feature of chromatographic or spectroscopic peaks. These algorithms are prone to miss detection of low
intensity peaks with a signal strength close to the noise level. To overcome these issues, techniques like smoothing, shape-matching and curve
fitting are often implemented and applied. At the time, the most promising approach to do shape-matching and noise reduction in one step uses the
continuous wavelet transformation (CWT).

In general, a CWT based approach describes a family of time-frequency-transformations often used in data compression and feature detection.
The term is coined by the use of a wavelet, as a basis function which is “compared” to the signal. The point of highest correlation between the
basis function and the signal reflects the location of the peak present. Due to the fact that MS derived peaks often follow the shape of a
gaussian distribution, the *Mexican Hat* wavelet as the negative normalized second derivative of the Gaussian distribution is perfectly
suited to find the peptide feature.

![](https://raw.githubusercontent.com/CSBiology/BIO-BTE-06-L-7/main/docs/img/Wavelets.png)

**Figure 5: Schematic representation of the ‘Haar’-wavelet (blue) and the ‘Mexican Hat’- wavelet (green). **
The ‘Haar’-wavelet is named after its discoverer Alfred Haar and represents the first wavelet ever to be described. The ‘Mexican Hat’- or ‘Ricker’-wavelet is
frequently used in the fields of signal detection and compression.

Depending on the quantification approach, the peptide features used for protein quantification might differ. In case of isotopic labeling,
quantification means pairing features with the proper mass shift according to the utilized label. It is essential to account for the frequency
of label incorporation when calculating the mass shift for the utilized label. Taking the ICAT method as an example, by which a heavy/light
difference of 9 Dalton per cysteine is incorporated, the total mass shift is 9 Dalton times the number of cysteine within the sequence.
Consequently, pairing peptide features for 15N labeling is even more challenging, as the mass shift is less discrete. Using stable
isotope labeling, different peptide feature pairs belonging to the same protein can be treated as technical replicates and averaged to gain
protein quantification. In contrast, the sum of all extracted peptide signals results in a label-free protein quantiﬁcation. Spectral counting
computes abundance values from the number of times a peptide was successfully identiﬁed by tandem mass spectrometry (MS/MS) and combines all
these events per protein. The spectral counting values can be normalized by the number of peptides theoretically expected from the particular
protein.

![](https://raw.githubusercontent.com/CSBiology/BIO-BTE-06-L-7/main/docs/img/ComputationalProteinQuantification.png)

**Figure 6: Computational strategy of peptide and protein quantiﬁcation on based on stable isotope labeling or by label-free quantiﬁcation.**
(A) Label-free methods compare corresponding peptide abundances over different MS runs. The abundance is either
estimated by the elution proﬁle les of the pep de ions or (B) in case of spectral counting, by the number of times a peptide was
successfully identiﬁed (MS2). In contrast, methods based on differential stable isotope labeling analyze peptides pairs detected by
their characteristic mass diﬀerence Δm/z. The abundance is estimated by the ratio of their corresponding elution proﬁles (C). Isobaric
tagging methods (D) compare the reporter ion abundances in the fragmentation spectrum.
### Targeted quantification

Targeted proteomics has gained significant popularity in mass spectrometry‐based protein quantification as a method to detect proteins of
interest with high sensitivity, quantitative accuracy and reproducibility. The two major strategies of (i) targeted acquisition at peptide,
and (ii) targeted data analysis at peptide ion level need to be distinguished.
###(i) Targeted acquisition at peptide

In multiple reaction monitoring (MRM or SRM for single/selected reaction monitoring) simply predefined transitions are recorded.
Knowledge about the targeted transitions from precursor to their corresponding fragment ions are needed and predefined in the mass
spectrometer. MRM can be performed rapidly and is highly specific even for low abundant peptide ions in complex mixtures, but with the
drawback of a necessary bias in the sense that only predefined peptides are measured.
### (ii) Targeted data analysis at peptide ion level

Data‐independent acquisition at the peptide level makes it possible to acquire peptide data for virtually all peptide ions present in a sample.
In this strategy, a high‐resolution mass analyzer—such as an orbitrap or a time‐of‐flight—is used to constantly sample the full mass range
at the peptide level during the entire chromatographic gradient. In a subsequent step, precursor ion chromatograms can be extracted by targeted
data analysis. Those extracted-ion chromatogram (XIC) can be obtained to calculate the area under the curve and used for peptide quantification.

Let’s start and extract a XIC…_____no_output_____

#r "nuget: FSharp.Stats, 0.4.0"
#r "nuget: BioFSharp, 2.0.0-beta5"
#r "nuget: BioFSharp.IO, 2.0.0-beta5"
#r "nuget: Plotly.NET, 2.0.0-beta6"
#r "nuget: System.Data.SQLite, 1.0.113.7"
#r "nuget: BioFSharp.Mz, 0.1.5-beta"
#r "nuget: MzIO, 0.1.0-beta"
#r "nuget: MzIO.SQL, 0.1.0-beta"
#r "nuget: MzIO.Processing, 0.1.0-beta"
#r "nuget: BIO-BTE-06-L-7_Aux, 0.0.1"

#r "nuget: Plotly.NET, 2.0.0-beta8"
#r "nuget: Plotly.NET.Interactive, 2.0.0-beta8"

open Plotly.NET
open FSharp.Stats
open BioFSharp
open System.IO
open System.Data.SQLite
open BIO_BTE_06_L_7_Aux.FS3_Aux_____no_output_____

We now want to extract the XIC for the peptide where we previously calculated the matching score.

Since we need several mass spectrometry scans to quantify over the retention time, we connect to our database
and index the entries according to their retention time._____no_output_____

// Code-Block 1
let directory = __SOURCE_DIRECTORY__
let path = Path.Combine[|directory;"downloads/sample.mzlite"|]
downloadFile path "sample.mzlite" "bio-bte-06-l-7"
let runID = "sample=0"

let mzReader = new MzIO.MzSQL.MzSQL(path)
let cn = mzReader.Open()
let transaction = mzReader.BeginTransaction()

// Indexes all spectra of the related sample run
let idx = MzIO.Processing.Query.getMS1RTIdx mzReader runID
idx_____no_output_____

**We know from the MS2 measurement, that our peptide had its match at a retention of around 51.95 min**. We create a query
to the database to extract the intensities of all peaks that are +/-5 min of our retention time and within 0.04 m/z of our peptide of interest.
After we are done, we close the connection to the database._____no_output_____

// Code-Block 2

let retentionTime = 51.95
let mzAtCharge2   = 511.2691141

let rtQuery = MzIO.Processing.Query.createRangeQuery retentionTime 5.

let mzQuery = MzIO.Processing.Query.createRangeQuery mzAtCharge2 0.04

let xic =
    MzIO.Processing.Query.getXIC mzReader idx rtQuery mzQuery
    |> Array.map (fun p -> p.Rt , p.Intensity)

transaction.Dispose()

let xicChart =
    xic
    |> Chart.Point
    |> Chart.withX_AxisStyle "Retention Time"
    |> Chart.withY_AxisStyle "Intensity/Score"
    |> Chart.withSize (900.,900.)
xicChart_____no_output_____

We have now the XIC in our hands and can use the second derivative to identify peaks with our trace._____no_output_____

// Code-Block 3

// get all peaks
let peaks =
    xic
    |> Array.unzip
    |> (fun (ret, intensity) ->
        FSharp.Stats.Signal.PeakDetection.SecondDerivative.getPeaks 0.1 2 13 ret intensity
        )

peaks |> Array.head_____no_output_____

The peak model includes numerus information. Therefore we can mark the apices of the peaks we identified._____no_output_____

// Code-Block 4

let apices =
    peaks
    |> Array.map (fun peak -> peak.Apex.XVal,peak.Apex.YVal)

let apicesChart=
    [
        Chart.Point(apices, Name="apices")
        |> Chart.withMarkerStyle(Size=15)
        Chart.Point(xic, Name = "XIC")

    ]
    |> Chart.Combine
    |> Chart.withX_AxisStyle "Retention Time"
    |> Chart.withY_AxisStyle "Intensity"
    |> Chart.withSize (900.,900.)
apicesChart_____no_output_____

We can then go ahead and characterize our peak and quantify the area under the fitted curve._____no_output_____

// Code-Block 5

// get peak at "ret=51.95" from all peaks "peaks"
let quantifiedXIC =
    BioFSharp.Mz.Quantification.HULQ.getPeakBy peaks retentionTime
    // quantify peak of interest
    |> BioFSharp.Mz.Quantification.HULQ.quantifyPeak

quantifiedXIC.Area_____no_output_____

The peak model gives us all the information we need for our peptide of interest. If we want to see what we quantified, we can take an
exponential modified gaussian function using the parameters given by the peak model and plot it together with the previously extracted XIC._____no_output_____

// Code-Block 6

let eval x =
    Fitting.NonLinearRegression.Table.emgModel.GetFunctionValue (vector quantifiedXIC.EstimatedParams) x

eval_____no_output_____// Code-Block 7

let quantifiedArea =
    xic
    |> Array.map (fun (rt,i) -> rt, eval rt)

let quantifiedAreaChart =
    [
        Chart.Point(xic,Name="XIC")
        Chart.SplineArea(quantifiedArea,Name="quantified XIC")
    ]
    |> Chart.Combine
    |> Chart.withX_AxisStyle (title = "Retention Time", MinMax = (51.,58.))
    |> Chart.withY_AxisStyle "Intensity"
    |> Chart.withSize (900.,900.)
quantifiedAreaChart_____no_output_____

## Questions

1. How does the Chart created by Code-Block 2 change, when you change the value of 'retentionTime' to 53.95? What does this parameter specify?
2. How does the Chart created by Code-Block 2 change, when you change the value of the parameter 'offset' from 5 to 10 or 20?
3. How does the Chart created by Code-Block 4 change, when you change the value of the parameter snr from 0.1 to 2.1?
What does this parameter specify, what does the abbreviation snr stand for?
4. How does the Chart created by Code-Block 7 change, when you change the value of the parameter retentionTime in CodeBlock 5 to 55.15?
5. Have a look at the peaks, how are the peaks shaped, are the shapes symmetric?
6. What does the term "peak tailing" imply.
7. What factors determine peak shape? Think of explanations (e.g. biochemical-interactions, detection method) for different peak shapes.
8. How many parameters does the model have (see quantifiedXIC.EstimatedParams, Code-Block 6), what does the abbreviation "EMG" stand for and
how is this function different from a gaussian function?
9. How could the fit created by the change in Code-Block 5, 6 and 8 profit from baseline correction?_____no_output_____