From 3788d8b5d95323c3806f10702ac766814d317943 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 30 Sep 2016 12:32:24 +0100 Subject: [PATCH] JAL-2234 FER1_ARATH renamed FER2_ARATH and vice versa --- examples/exampleFeatures.txt | 26 +++++++++++++------------- examples/plantfdx.fa | 12 ++++++------ examples/plantfdx.features | 22 +++++++++++----------- examples/uniref50.fa | 12 ++++++------ 4 files changed, 36 insertions(+), 36 deletions(-) diff --git a/examples/exampleFeatures.txt b/examples/exampleFeatures.txt index c0098a9..2de9817 100755 --- 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 Fer2 Status: True Positive Pfam 8_8 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 -Fer2 Status: True Positive Pfam 60_13 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 +Fer2 Status: True Positive Pfam 60_13 FER1_ARATH -1 60 135 Pfam +Ferredoxin_fold Status: True Positive FER1_ARATH -1 50 145 Cath Fer2 Status: True Positive Pfam 60_11 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 High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 112_11 FER1_SPIOL -1 112 112 PHOSPHORYLATION (S) High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 139_13 FER1_SPIOL -1 139 139 PHOSPHORYLATION (T) High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 73_7 FER1_SPIOL -1 73 73 PHOSPHORYLATION (Y) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 19_1 FER1_ARATH -1 19 19 PHOSPHORYLATION (S) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 24_2 FER1_ARATH -1 24 24 PHOSPHORYLATION (S) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER1_ARATH -1 90 90 PHOSPHORYLATION (S) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 FER1_ARATH -1 107 107 PHOSPHORYLATION (S) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER1_ARATH -1 114 114 PHOSPHORYLATION (S) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER1_ARATH -1 141 141 PHOSPHORYLATION (T) -High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 75_7 FER1_ARATH -1 75 75 PHOSPHORYLATION (Y) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 19_1 FER2_ARATH -1 19 19 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 24_2 FER2_ARATH -1 24 24 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 90_9 FER2_ARATH -1 90 90 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 107_10 FER2_ARATH -1 107 107 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 114_11 FER2_ARATH -1 114 114 PHOSPHORYLATION (S) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 141_14 FER2_ARATH -1 141 141 PHOSPHORYLATION (T) +High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (Y) 75_7 FER2_ARATH -1 75 75 PHOSPHORYLATION (Y) High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 38_3 FER_BRANA -1 38 38 PHOSPHORYLATION (S) High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (S) 62_6 FER_BRANA -1 62 62 PHOSPHORYLATION (S) High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8 FER_BRANA -1 89 89 PHOSPHORYLATION (T) diff --git a/examples/plantfdx.fa b/examples/plantfdx.fa index 1412a5a..f314c85 100644 --- 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 --- 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 Description: Fer2 Status: True Positive Pfam 8_83 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 -Description: Fer2 Status: True Positive Pfam 60_135 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 -Description: Fer2 Status: True Positive Pfam 8_83 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 Description: Fer2 Status: True Positive Pfam 60_135 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 +Description: Fer2 Status: True Positive Pfam 8_83 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 +Description: Fer2 Status: True Positive Pfam 60_135 FER1_ARATH -1 60 135 Pfam Description: Fer2 Status: True Positive Pfam 60_118 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 --- 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------------------- -- 1.7.10.2