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Changeset 2:814b453382cf (2017-01-23)

Previous changeset 1:029e38c5063a (2017-01-23) Next changeset 3:baeab8664657 (2017-02-06)

Commit message:
Uploaded

added:
test-data/nad3.pir
test-data/nad3.pir-gb
test-data/nad3.pir-gb.htm

diff -r 029e38c5063a -r 814b453382cf test-data/nad3.pir
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nad3.pir Mon Jan 23 07:42:56 2017 -0500

@@ -0,0 +1,101 @@
+>P1;nad3_parde
+
+------MEYLLQEYLPILVFLGMASALAIVLILAAAVIAVRN--PDPEKVSAYECGFNAF
+D-DARMKFDVRFYLVSILFIIFDLEVAFLFPWAVSFASLS-DVAFWGLMVFLAVLTVGFA
+YEWKKGALEWA----------------------*
+
+>P1;nad3_acaca
+
+---------MTLEYIYIFIFFWGAFFISCLLIFLSYFLVYQE--SDIEKNSAYECGFQPF
+E-DTRSKFNVRYYLIAILFMIFDLEIMYLFPWSISISTGS-FFGVWAIFLFLIILTVGFI
+YEWQKGALEWD----------------------*
+
+>P1;nad3_allma
+
+--------------MTYLVYIVFTIVLTVGLILVSYLLSQAQ--PDSEKVSAYECGFSPL
+G-DARQKFDVSFYLIAILFIIFDLEVVFILPFASVIHNVS-LLGGWITIIFLVILTIGFI
+YEFVSGAITDSF---------------------*
+
+>P1;nad3_apec
+
+-----------IFNFLTLFVSILIFLITTLITFAAHFLPSRN-TD-SEKSSPYECGFDPL
+N-SARVPFSFRFFLVAILFLLFDLEIALLFPLPFSVFFH--P--IHTP----LILTVGLI
+FEWVQGGLDWAE---------------------*
+
+>P1;nad3_arath
+
+---------MMSEFAPISIYLVISLLVSLILLGVPFPFASNS-STYPEKLSAYECGFDPS
+G-DARSRFDIRFYLVSILFLIPDLEVTFFFPWAVPPNKID-LFGFWSMMAFLFILTIGFL
+YEWKRGASDRE----------------------*
+
+>P1;nad3_balca
+
+-------------MNSFLIYLLIAITLSFILSIVGHRLPTRN-MD-QEKLSPYECGFDPQ
+A-SARLPFSLRFFLVAILFLLFDLEIALLLPFPAALSARDPQLSFTLAFLILLILTIGLI
+YEWMEGGLEWAE---------------------*
+
+>P1;nad3_chocr
+
+------MKLIFTEYSAILIFFAISSLLSSVIFLLSYFLIPQK--PDQEKVSAYECGFNPF
+D-DARATFDIRFYLVAILFLIFDLEISFLFPWSLVLGEIS-IIGFWSMIVFLVILTIGFI
+YEWYKGALEWE----------------------*
+
+>P1;nad3_drome
+
+-------------MFSIIFIALLILLITTIVMFLASILSKKA-LIDREKSSPFECGFDPK
+S-SSRLPFSLRFFLITIIFLIFDVEIALILPMIIIMKYSNIMIWTITSIIFILILLIGLY
+HEWNQGMLNWSN---------------------*
+
+>P1;nad3_human
+
+-------------MN-FALILMINTLLALLLMIITFWLPQLN-GY-MEKSTPYECGFDPM
+S-PARVPFSMKFFLVAITFLLFDLEIALLLPLPWALQTTNLPLMVMSSLLLIIILALSLA
+YEWLQKGLDWTE---------------------*
+
+>P1;nad3_ktun
+
+-------------MFFVLSLVLFTFLLSLVLLSVSLSLTKKK-MMNREKSSPFECGFDPK
+S-SARLPFSMRFFLITVVFLVFDVEIVLLLPYLFSSGWSIDVFSLVGSMMILVILIIGVL
+HEWSEGSLEWFSSSN------------------*
+
+>P1;nad3_lter
+
+-------------MILTALSSAIALLVPIIILGAAWVLASRS-TEDREKSSPFECGFDPK
+S-TARIPFSTRFFLLAIIFIVFDIEIVLLMPLPTILHTSDVFTTVTTSVLFLMILLIGLI
+HEWKEGSLDWSS---------------------*
+
+>P1;nad3_marpo
+
+-----------MEFAPIFVYLVISLLLSLILIGVSFLFASSSSLAYPEKLSAYECGFDPF
+D-DARSRFDIRFYLVSILFIIFDLEVTFLFPWAVSLNKIG-LFGFWSMMVFLFILTIGFV
+YEWKKGALDWE----------------------*
+
+>P1;nad3_metse
+
+---------MYTEFYGILVLLIFSVVLSAIISGASYILGDKQ--PDREKVSAYECGFDPF
+G-TPGRPFSIRFFLIGILFLIFDLEISFLFPWCVVCNQVF-PFGYWTMIVFLAVLTLGLV
+YEWLKGGLEWE----------------------*
+
+>P1;nad3_picca
+
+MLNYFVYPYGIENDMGMKFYMMLVPMMSMVLMMINYMMTNKS-DNNMNKTGPYECGFDSF
+R-QSRTTYSIKFILIAILFLPFDLELTSILPYTLSMYNTN-IYGLFILLYFLLPLIIGFI
+IEINTKAIYMTKMFNRNVKSMTSYVKYNNKI--*
+
+>P1;nad3_podan
+
+-------------MSSMTLFILFVSIIALLFLFINLIFAPHN--PYQEKYSIFECGFHSF
+LGQNRTQFGVKFFIFALVYLLLDLEILLTFPFAVSEYVNN-IYGLIILLGFITIITIGFV
+YELGKSALKIDSRQVITMTRFNYSSTIEYLGKI*
+
+>P1;nad3_prowi
+
+----------MYEFLGILIYFFIALALSLLLLGLPFLVSTRK--ADPEKISAYECGFDPF
+D-DARGRFDIQFYLVAILFIIFDLEVAFLFPWALTLNKIG-YFGFWSMMLFLFILTVGFI
+YEWRKGALDWS----------------------*
+
+>P1;nad3_recam
+
+-----MNTMILSEYLSVLIFFIFSFGLSCIILGLSYVLATQN--ADTEKLSPYECGFNPF
+D-DARGAFDVRFYLVAILFIIFDLEVAFLFPWAVALSDVT-IFGFWTMFIFLLILTVGFI
+YEWKKGALDWE----------------------*

diff -r 029e38c5063a -r 814b453382cf test-data/nad3.pir-gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nad3.pir-gb Mon Jan 23 07:42:56 2017 -0500

@@ -0,0 +1,68 @@
+>P1;nad3_parde
+
+EKVSAYECGF NAFARMKFDV RFYLVSILFI IFDLEVAFLF PVLTVGFAYE WKKGAL*
+
+>P1;nad3_acaca
+
+EKNSAYECGF QPFTRSKFNV RYYLIAILFM IFDLEIMYLF PILTVGFIYE WQKGAL*
+
+>P1;nad3_allma
+
+EKVSAYECGF SPLARQKFDV SFYLIAILFI IFDLEVVFIL PILTIGFIYE FVSGAI*
+
+>P1;nad3_apec
+
+EKSSPYECGF DPLARVPFSF RFFLVAILFL LFDLEIALLF PILTVGLIFE WVQGGL*
+
+>P1;nad3_arath
+
+EKLSAYECGF DPSARSRFDI RFYLVSILFL IPDLEVTFFF PILTIGFLYE WKRGAS*
+
+>P1;nad3_balca
+
+EKLSPYECGF DPQARLPFSL RFFLVAILFL LFDLEIALLL PILTIGLIYE WMEGGL*
+
+>P1;nad3_chocr
+
+EKVSAYECGF NPFARATFDI RFYLVAILFL IFDLEISFLF PILTIGFIYE WYKGAL*
+
+>P1;nad3_drome
+
+EKSSPFECGF DPKSRLPFSL RFFLITIIFL IFDVEIALIL PILLIGLYHE WNQGML*
+
+>P1;nad3_human
+
+EKSTPYECGF DPMARVPFSM KFFLVAITFL LFDLEIALLL PILALSLAYE WLQKGL*
+
+>P1;nad3_ktun
+
+EKSSPFECGF DPKARLPFSM RFFLITVVFL VFDVEIVLLL PILIIGVLHE WSEGSL*
+
+>P1;nad3_lter
+
+EKSSPFECGF DPKARIPFST RFFLLAIIFI VFDIEIVLLM PILLIGLIHE WKEGSL*
+
+>P1;nad3_marpo
+
+EKLSAYECGF DPFARSRFDI RFYLVSILFI IFDLEVTFLF PILTIGFVYE WKKGAL*
+
+>P1;nad3_metse
+
+EKVSAYECGF DPFPGRPFSI RFFLIGILFL IFDLEISFLF PVLTLGLVYE WLKGGL*
+
+>P1;nad3_picca
+
+NKTGPYECGF DSFSRTTYSI KFILIAILFL PFDLELTSIL PPLIIGFIIE INTKAI*
+
+>P1;nad3_podan
+
+EKYSIFECGF HSFNRTQFGV KFFIFALVYL LLDLEILLTF PIITIGFVYE LGKSAL*
+
+>P1;nad3_prowi
+
+EKISAYECGF DPFARGRFDI QFYLVAILFI IFDLEVAFLF PILTVGFIYE WRKGAL*
+
+>P1;nad3_recam
+
+EKLSPYECGF NPFARGAFDV RFYLVAILFI IFDLEVAFLF PILTVGFIYE WKKGAL*
+

diff -r 029e38c5063a -r 814b453382cf test-data/nad3.pir-gb.htm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nad3.pir-gb.htm Mon Jan 23 07:42:56 2017 -0500

[

b'@@ -0,0 +1,124 @@\n+<html>\n+<head>\n+<meta http-equiv=content-type content=text/html;charset=ISO-8859-1>\n+<title>nad3.pir</title>\n+<style media=screen type=text/css></style>\n+</head>\n+\n+<body bgcolor=#f5f5a3>\n+<h2>Gblocks 0.91b Results</h2>\n+\n+Processed file: nad3.pir \n+Number of sequences: 17 Alignment assumed to be: Protein \n+New number of positions: 56 (selected positions are underlined in blue)\n+\n+<pre>\n+ 10 20 30 40 50 60\n+ =========+=========+=========+=========+=========+=========+\n+nad3_parde ------MEYLLQEYLPILVFLGMASALAIVLILAAAVIAVRN--PDPEKVSAYECGFNAF\n+nad3_acaca ---------MTLEYIYIFIFFWGAFFISCLLIFLSYFLVYQE--SDIEKNSAYECGFQPF\n+nad3_allma --------------MTYLVYIVFTIVLTVGLILVSYLLSQAQ--PDSEKVSAYECGFSPL\n+nad3_apec -----------IFNFLTLFVSILIFLITTLITFAAHFLPSRN-TD-SEKSSPYECGFDPL\n+nad3_arath ---------MMSEFAPISIYLVISLLVSLILLGVPFPFASNS-STYPEKLSAYECGFDPS\n+nad3_balca -------------MNSFLIYLLIAITLSFILSIVGHRLPTRN-MD-QEKLSPYECGFDPQ\n+nad3_chocr ------MKLIFTEYSAILIFFAISSLLSSVIFLLSYFLIPQK--PDQEKVSAYECG#######\n+\n+\n+ 130 140 150\n+ =========+=========+=========+===\n+nad3_parde YEWKKGALEWA----------------------\n+nad3_acaca YEWQKGALEWD----------------------\n+nad3_allma YEFVSGAITDSF---------------------\n+nad3_apec FEWVQGGLDWAE---------------------\n+nad3_arath YEWKRGASDRE----------------------\n+nad3_balca YEWMEGGLEWAE---------------------\n+nad3_chocr YEWYKGALEWE----------------------\n+nad3_drome HEWNQGMLNWSN---------------------\n+nad3_human YEWLQKGLDWTE---------------------\n+nad3_ktun HEWSEGSLEWFSSSN------------------\n+nad3_lter HEWKEGSLDWSS---------------------\n+nad3_marpo YEWKKGALDWE----------------------\n+nad3_metse YEWLKGGLEWE----------------------\n+nad3_picca IEINTKAIYMTKMFNRNVKSMTSYVKYNNKI--\n+nad3_podan YELGKSALKIDSRQVITMTRFNYSSTIEYLGKI\n+nad3_prowi YEWRKGALDWS----------------------\n+nad3_recam YEWKKGALDWE----------------------\n+ ######## \n+\n+\n+\n+</pre>\n+<pre>\n+\n+\n+ Parameters used\n+Minimum Number Of Sequences For A Conserved Position: 9\n+Minimum Number Of Sequences For A Flanking Position: 14\n+Maximum Number Of Contiguous Nonconserved Positions: 8\n+Minimum Length Of A Block: 5\n+Allowed Gap Positions: None\n+Use Similarity Matrices: Yes\n+\n+</pre><pre>Flank positions of the 3 selected block(s)\n+Flanks: [48 60] [64 91] [114 128] \n+\n+New number of positions in nad3.pir-gb1: 56 (36% of the original 153 positions)\n+\n+\n+</body>\n+</html>\n'