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JAL-2234 FER1_ARATH renamed FER2_ARATH and vice versa
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Fri, 30 Sep 2016 11:32:24 +0000 (12:32 +0100)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Fri, 30 Sep 2016 11:32:24 +0000 (12:32 +0100)
examples/exampleFeatures.txt patch | blob | history
examples/plantfdx.fa patch | blob | history
examples/plantfdx.features patch | blob | history
examples/uniref50.fa patch | blob | history

diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt
index c0098a9..2de9817 100755 (executable)
--- a/examples/exampleFeatures.txt
+++ b/examples/exampleFeatures.txt
@@ -79,12 +79,12 @@ Iron-sulfur (2Fe-2S)        FER_BRANA       -1      47      47      METAL
 Iron-sulfur (2Fe-2S)   FER_BRANA       -1      77      77      METAL
 <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_8</a></html>     FER_BRANA       -1      8       83      Pfam
 Ferredoxin_fold Status: True Positive  FER_BRANA       -1      2       96      Cath
-Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      91      91      METAL
-Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      96      96      METAL
-Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      99      99      METAL
-Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      129     129     METAL
-<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html>   FER2_ARATH      -1      60      135     Pfam
-Ferredoxin_fold Status: True Positive  FER2_ARATH      -1      50      145     Cath
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      91      91      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      96      96      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      99      99      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      129     129     METAL
+<html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_13</a></html>   FER1_ARATH      -1      60      135     Pfam
+Ferredoxin_fold Status: True Positive  FER1_ARATH      -1      50      145     Cath
 <html>Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_11</a></html>   Q93Z60_ARATH    -1      60      118     Pfam
 Ferredoxin_fold Status: True Positive  Q93Z60_ARATH    -1      52      118     Cath
 Iron-sulfur (2Fe-2S)   FER1_MAIZE      -1      91      91      METAL
@@ -127,13 +127,13 @@ STARTGROUP        netphos
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 112_11</a></html>     FER1_SPIOL      -1      112     112     PHOSPHORYLATION (S)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 139_13</a></html>     FER1_SPIOL      -1      139     139     PHOSPHORYLATION (T)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00221&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 73_7</a></html>       FER1_SPIOL      -1      73      73      PHOSPHORYLATION (Y)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html>   FER1_ARATH      -1      19      19      PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html>   FER1_ARATH      -1      24      24      PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html>   FER1_ARATH      -1      90      90      PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER1_ARATH      -1      107     107     PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER1_ARATH      -1      114     114     PHOSPHORYLATION (S)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER1_ARATH      -1      141     141     PHOSPHORYLATION (T)
-<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER1_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html>   FER1_ARATH      -1      75      75      PHOSPHORYLATION (Y)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 19_1</a></html>   FER2_ARATH      -1      19      19      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 24_2</a></html>   FER2_ARATH      -1      24      24      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 90_9</a></html>   FER2_ARATH      -1      90      90      PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 107_10</a></html> FER2_ARATH      -1      107     107     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 114_11</a></html> FER2_ARATH      -1      114     114     PHOSPHORYLATION (S)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 141_14</a></html> FER2_ARATH      -1      141     141     PHOSPHORYLATION (T)
+<html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=FER2_ARATH&amp;service=NetPhos-2.0">PHOSPHORYLATION (Y) 75_7</a></html>   FER2_ARATH      -1      75      75      PHOSPHORYLATION (Y)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 38_3</a></html>       FER_BRANA       -1      38      38      PHOSPHORYLATION (S)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (S) 62_6</a></html>       FER_BRANA       -1      62      62      PHOSPHORYLATION (S)
 <html>High confidence server. Only hits with scores over 0.8 are reported. <a href="http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P00227&amp;service=NetPhos-2.0">PHOSPHORYLATION (T) 89_8</a></html>       FER_BRANA       -1      89      89      PHOSPHORYLATION (T)
diff --git a/examples/plantfdx.fa b/examples/plantfdx.fa
index 1412a5a..f314c85 100644 (file)
--- a/examples/plantfdx.fa
+++ b/examples/plantfdx.fa
@@ -35,17 +35,17 @@ IETHKEEELTA-
 EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDVT
 IETHREEDMV--
 >FER1_ARATH/1-148
-----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
-EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
-IETHKEEDIV--
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
+IETHKEEAIM--
 >FER_BRANA/1-96
 ----------------------------------------------------------ATYKVKFITPEGEQ
 EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDVT
 IETHKEEELV--
 >FER2_ARATH/1-148
-----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
-EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDVV
-IETHKEEAIM--
+----MASTALSSAIVGTSFIRRSPAPISLRSLPSANT-QSLFGLKS-GTARGGRVTAMATYKVKFITPEGEL
+EVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDVT
+IETHKEEDIV--
 >Q93Z60_ARATH/1-118
 ----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
 EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD--------------------
diff --git a/examples/plantfdx.features b/examples/plantfdx.features
index 872dadc..6a2e058 100644 (file)
--- a/examples/plantfdx.features
+++ b/examples/plantfdx.features
@@ -78,23 +78,23 @@ Iron-sulfur (2Fe-2S)        FER3_RAPSA      -1      77      77      METAL
 R -> K         FER3_RAPSA      -1      91      91      VARIANT
 M -> V         FER3_RAPSA      -1      95      95      VARIANT
 <html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_83</a></html>       FER3_RAPSA      -1      8       83      Pfam
-Chloroplast    FER1_ARATH      -1      1       52      TRANSIT
-Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      91      91      METAL
-Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      96      96      METAL
-Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      99      99      METAL
-Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      129     129     METAL
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_135</a></html>     FER1_ARATH      -1      60      135     Pfam
-Iron-sulfur (2Fe-2S)   FER_BRANA       -1      39      39      METAL
-Iron-sulfur (2Fe-2S)   FER_BRANA       -1      44      44      METAL
-Iron-sulfur (2Fe-2S)   FER_BRANA       -1      47      47      METAL
-Iron-sulfur (2Fe-2S)   FER_BRANA       -1      77      77      METAL
-<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_83</a></html>       FER_BRANA       -1      8       83      Pfam
 Chloroplast    FER2_ARATH      -1      1       52      TRANSIT
 Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      91      91      METAL
 Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      96      96      METAL
 Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      99      99      METAL
 Iron-sulfur (2Fe-2S)   FER2_ARATH      -1      129     129     METAL
 <html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_135</a></html>     FER2_ARATH      -1      60      135     Pfam
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      39      39      METAL
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      44      44      METAL
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      47      47      METAL
+Iron-sulfur (2Fe-2S)   FER_BRANA       -1      77      77      METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 8_83</a></html>       FER_BRANA       -1      8       83      Pfam
+Chloroplast    FER1_ARATH      -1      1       52      TRANSIT
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      91      91      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      96      96      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      99      99      METAL
+Iron-sulfur (2Fe-2S)   FER1_ARATH      -1      129     129     METAL
+<html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_135</a></html>     FER1_ARATH      -1      60      135     Pfam
 <html>Description: Fer2 Status: True Positive <a href="http://pfam.xfam.org/family/PF00111">Pfam 60_118</a></html>     Q93Z60_ARATH    -1      60      118     Pfam
 Chloroplast    FER1_MAIZE      -1      1       52      TRANSIT
 STRAND FER1_MAIZE      -1      57      59      STRAND
diff --git a/examples/uniref50.fa b/examples/uniref50.fa
index 72c062d..4bdbfb4 100755 (executable)
--- a/examples/uniref50.fa
+++ b/examples/uniref50.fa
@@ -35,17 +35,17 @@ TIETHKEEELTA-
 QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV
 TIETHREEDMV--
 >FER1_ARATH Ferredoxin-1, chloroplast precursor
-MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
-LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
-TIETHKEEDIV--
+MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
+QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
+VIETHKEEAIM--
 >FER_BRANA Ferredoxin
 -----------------------------------------------------------ATYKVKFITPEGE
 QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV
 TIETHKEEELV--
 >FER2_ARATH Ferredoxin-2, chloroplast precursor
-MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
-QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV
-VIETHKEEAIM--
+MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE
+LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV
+TIETHKEEDIV--
 >Q93Z60_ARATH At1g10960/T19D16_12
 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE
 QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD-------------------