From 2965d436b339902fa02f6233f02d049e6a8151b6 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 11 Mar 2015 08:44:08 +0000 Subject: [PATCH] JAL-1684 applet example for SplitFrame view of cDNA/Protein --- examples-jbake/templates/jvl_examples.ftl | 19 +++ examples/applets.html | 23 +++ examples/estrogenReceptorCdna.fa | 221 +++++++++++++++++++++++++++++ examples/estrogenReceptorProtein.fa | 81 +++++++++++ 4 files changed, 344 insertions(+) create mode 100644 examples/estrogenReceptorCdna.fa create mode 100644 examples/estrogenReceptorProtein.fa diff --git a/examples-jbake/templates/jvl_examples.ftl b/examples-jbake/templates/jvl_examples.ftl index f2bf8b1..d5e328e 100644 --- a/examples-jbake/templates/jvl_examples.ftl +++ b/examples-jbake/templates/jvl_examples.ftl @@ -85,4 +85,23 @@ Try out JalviewLite by pressing one of the buttons below.
secondary structure annotation +

+

Linked amino acid and cDNA alignments for homologous proteins

+

+ + + + + +
<@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" + , "file":"estrogenReceptorCdna.fa" + , "file2":"estrogenReceptorProtein.fa" + , "defaultColour":"Purine/Pyrimidine" + , "showAnnotation":"true" + , "windowHeight":"800" + , "windowWidth":"650" + , "showConservation":"false" + , "showQuality":"false" + , "showConsensus":"true" + , "showFullId":"false"} prots=true />Displays a split window view of protein and its related cDNA
diff --git a/examples/applets.html b/examples/applets.html index cc85e86..7044253 100755 --- a/examples/applets.html +++ b/examples/applets.html @@ -313,6 +313,29 @@ Try out JalviewLite by pressing one of the buttons below.
secondary structure annotation +

+

Linked amino acid and cDNA alignments for homologous proteins

+

+ + + + + +
+ + + + + + + + + + +Displays a split window view of protein and its related cDNA
diff --git a/examples/estrogenReceptorCdna.fa b/examples/estrogenReceptorCdna.fa new file mode 100644 index 0000000..9d857db --- /dev/null +++ b/examples/estrogenReceptorCdna.fa @@ -0,0 +1,221 @@ +>EMBLCDS|ADZ17331/1-1593 Homo sapiens (human) estrogen nuclear receptor beta variant a +atggatataaaaaactcaccatctagccttaattctccttcctcctacaactgcagtcaatccatcttaccc +ctggagcacggctccatatacataccttcctcctatgtagacagccaccatgaatatccagccatgacattc +tatagccctgctgtgatgaattacagcattcccagcaatgtcactaacttggaaggtgggcctggtcggcag +accacaagcccaaatgtgttgtggccaacacctgggcacctttctcctttagtggtccatcgccagttatca +catctgtatgcggaacctcaaaagagtccctggtgtgaagcaagatcgctagaacacaccttacctgtaaac +agagagacactgaaaaggaaggttagtgggaaccgttgcgccagccctgttactggtccaggttcaaagagg +gatgctcacttctgcgctgtctgcagcgattacgcatcgggatatcactatggagtctggtcgtgtgaagga +tgtaaggccttttttaaaagaagcattcaaggacataatgattatatttgtccagctacaaatcagtgtaca +atcgataaaaaccggcgcaagagctgccaggcctgccgacttcggaagtgttacgaagtgggaatggtgaag +tgtggctcccggagagagagatgtgggtaccgccttgtgcggagacagagaagtgccgacgagcagctgcac +tgtgccggcaaggccaagagaagtggcggccacgcgccccgagtgcgggagctgctgctggacgccctgagc +cccgagcagctagtgctcaccctcctggaggctgagccgccccatgtgctgatcagccgccccagtgcgccc +ttcaccgaggcctccatgatgatgtccctgaccaagttggccgacaaggagttggtacacatgatcagctgg +gccaagaagattcccggctttgtggagctcagcctgttcgaccaagtgcggctcttggagagctgttggatg +gaggtgttaatgatggggctgatgtggcgctcaattgaccaccccggcaagctcatctttgctccagatctt +gttctggacagggatgaggggaaatgcgtagaaggaattctggaaatctttgacatgctcctggcaactact +tcaaggtttcgagagttaaaactccaacacaaagaatatctctgtgtcaaggccatgatcctgctcaattcc +agtatgtaccctctggtcacagcgacccaggatgctgacagcagccggaagctggctcacttgctgaacgcc +gtgaccgatgctttggtttgggtgattgccaagagcggcatctcctcccagcagcaatccatgcgcctggct +aacctcctgatgctcctgtcccacgtcaggcatgcgagtaacaagggcatggaacatctgctcaacatgaag +tgcaaaaatgtggtcccagtgtatgacctgctgctggagatgctgaatgcccacgtgcttcgcgggtgcaag +tcctccatcacggggtccgagtgcagcccggcagaggacagtaaaagcaaagagggctcccagaacccacag +tctcagtga +>EMBLCDS|AAK93056/1-1455 Drosophila melanogaster (fruit fly) GH28308p +atgtccgacggcgtcagcatcttgcacatcaaacaggaggtggacactccatcggcgtcctgctttagtccc +agctccaagtcaacggccacgcagagtggcacaaacggcctgaaatcctcgccctcggtttcgccggaaagg +cagctctgcagctcgacgacctctctatcctgcgatttgcacaatgtatccttaagcaatgatggcgatagt +ctgaaaggaagtggtacaagtggcggcaatggcggaggaggaggtggtggtacgagtggtggaaatgcgacc +aatgcgagtgccggagctggatcgggatccgtcagggacgagctccgccgattgtgtttggtttgtggcgat +gtggccagtggattccactatggtgtggcgagttgtgaggcttgcaaagcgttctttaaacgcaccatccaa +ggcaacatcgagtacacgtgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgccaa +gcgtgtcgcttccagaaatgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgtgga +ggacggcagaagtaccgaaggaatcctgtatcaaactcttaccagactatgcagctgctataccaatccaac +accacctcgctgtgcgatgtcaagatactggaggtgctcaattcatatgagccggatgccttgagcgtccaa +acgccgccgccgcaagtccacacgactagcataactaatgatgaggcctcatcctcctcgggcagcataaaa +ctggagtccagcgttgttacgcccaatgggacttgcattttccaaaacaacaacaacaatgatcccaatgag +atactaagcgtccttagtgatatttacgacaaggaattggtcagcgtcattggctgggccaagcagatacct +ggctttatagatctgccacttaacgaccagatgaagcttctccaggtgtcgtgggcagagatcctgacgctc +cagctgaccttccggtccctaccgttcaatggcaagttatgcttcgccacggatgtctggatggatgaacat +ttggccaaggagtgcggttacacggagttctactaccactgcgtccagatcgcacagcgcatggaaagaata +tcgccacgaagggaggagtactacttgctaaaggcgctcctgctggccaactgcgacattctgctggatgat +cagagttccctgcgcgcatttcgtgatacgattcttaattctctaaacgatgtggtctacttgctgcgtcat +tcgtcggccgtgtcgcatcagcaacaattgctgcttttgctgccttcgctgcggcaggcggatgatatcctg +cgaagattttggcgtggaattgcacgcgatgaagtcattaccatgaagaaactgttcctcgagatgctcgag +ccgctggccaggtga +>EMBLCDS|BAA89539/1-2133 Anguilla japonica (Japanese eel) progesterone receptor +atggacaacaatcaccaagacaagatggaaagtctatacacgccagccagagcatcaccaactcctgatgca +gaatcgattaaaagagccaggaatttgattaaaacatactcggagtcttttgggagttatgtggaggagata +gttcgagacgactcgaataacatacaatctttgagcagcgtccctctcttgatgcgtaattttggaaacatg +gacaccctaacctgcgcacctggctcgggtagtgacagtgagatttggaaagactttgttgttcccgggaac +tctgtggtaagcaaagacacctgtggtcatgttgaaatatccactaaagccgaaaatttgtcttgggctgcc +gcgcccttaagtagagaagaaaccctcgcgaaaggaactgttacggtcccagcgactgtgcctaaagaaagt +tttaccgcaacatcaaacacttcttcagccagtggaatctctattaaagatgaacaacaatctttgctcaaa +atggaaccacagtcttctgacttttgtccttatacagcaaatataccgaaattgaatccatcttatctgacc +aatactgcgagtacgaaacaacttggatatggcgaacagccggacacttcagcgcactcctctccacctgct +cagaagattgttttagatactgctcgatactcggccgatttatgttcggataaccctttaccgcaagcgaca +aatatcaaaacagatccttgtagtagtttctcttctttcgttggagaagggatccttactagggcatctatg +ggctactcacagcaagcgattcagacattgccggtgcacaagagtgaaccgttcaggttgtctgcttcgagc +gcgcccgcggattctccgttttggtgccaatccacgggtccttctgaggatcatcatctgcagattgactat +ctatctcccgctggactccacagcacatgcaaatacagttccacgaacgcgtacagctcctatttaggtgtg +ctgccccagagggtgtgcgtcatctgtggggatgaagcatcaggctgtcactatggtgtcctcacctgtggc +agctgtaaggtgttctttaagagggcagtggaaggccatcataactacttgtgtgctggacggaatgactgc +atcgtggacaagatccgtaggaaaaactgtcctgcttgtcgcctcagaaagtgctaccaggcgggaatgata +ctgggaggtcggaagctgaagaagttgggggctctgaaggcagcagggctgacccaggccctggtggcccac +tcactgactcctcggaggctctctggtgacagccaggccctgatgcccctgggctgccttccaggggtccgg +gagctgcacctttccccacagatcatcagcgtgctggagagcattgagcctgaggtggtgtactctggttat +gacaactcccagcctgacatgcccaatatgctgctcaacagcctcaaccgcttatgtgagaggcagctgctg +aggattgtcaagtggtccaagtctttaccaggttttcgcagtttacacatcaatgaccaaatggctctgatc +cagtactcctggatgagcttaatggtattttctttgggttggcggtctttccaaaatgtcaccagtgattac +ctgtactttgcacctgacctcattctcaacgaagagtatatgaggaggtctccaatatttgacctgtgcatg +gccatgcagttcatccctcaagagtttgccaatctccaggtgaccaaggaggagtttctgtgcatgaaggtc +ttgctgttgctcaacacagtgcctctggaggggttgaagagccagccacagtttgatgagatgaggcagaat +tacatccatgaactcaccaaggccattcacctgcgagagaatggtgtggtcgcctgctcccagcgtttctac +cacctgaccaagctgatggaccacatgcatgacattgtgaagaagctccacctgtactgcctgagcactttc +attcaggcagatgccatgcgggtagagttccccgagatgatgtcagaagtcatcgcctcccagctgcctcgg +gtgctcgctggaatggtgaaaccccttctttttcacaccaaatga +>EMBLCDS|AHW56473/1-1590 Homo sapiens (human) partial estrogen receptor 2 isoform A +atggatataaaaaactcaccatctagccttaattctccttcctcctacaactgcagtcaatccatcttaccc +ctggagcacggctccatatacataccttcctcctatgtagacagccaccatgaatatccagccatgacattc +tatagccctgctgtgatgaattacagcattcccagcaatgtcactaacttggaaggtgggcctggtcggcag +accacaagcccaaatgtgttgtggccaacacctgggcacctttctcctttagtggtccatcgccagttatca +catctgtatgcggaacctcaaaagagtccctggtgtgaagcaagatcgctagaacacaccttacctgtaaac +agagagacactgaaaaggaaggttagtgggaaccgttgcgccagccctgttactggtccaggttcaaagagg +gatgctcacttctgcgctgtctgcagcgattacgcatcgggatatcactatggagtctggtcgtgtgaagga +tgtaaggccttttttaaaagaagcattcaaggacataatgattatatttgtccagctacaaatcagtgtaca +atcgataaaaaccggcgcaagagctgccaggcctgccgacttcggaagtgttacgaagtgggaatggtgaag +tgtggctcccggagagagagatgtgggtaccgccttgtgcggagacagagaagtgccgacgagcagctgcac +tgtgccggcaaggccaagagaagtggcggccacgcgccccgagtgcgggagctgctgctggacgccctgagc +cccgagcagctagtgctcaccctcctggaggctgagccgccccatgtgctgatcagccgccccagtgcgccc +ttcaccgaggcctccatgatgatgtccctgaccaagttggccgacaaggagttggtacacatgatcagctgg +gccaagaagattcccggctttgtggagctcagcctgttcgaccaagtgcggctcttggagagctgttggatg +gaggtgttaatgatggggctgatgtggcgctcaattgaccaccccggcaagctcatctttgctccagatctt +gttctggacagggatgaggggaaatgcgtagaaggaattctggaaatctttgacatgctcctggcaactact +tcaaggtttcgagagttaaaactccaacacaaagaatatctctgtgtcaaggccatgatcctgctcaattcc +agtatgtaccctctggtcacagcgacccaggatgctgacagcagccggaagctggctcacttgctgaacgcc +gtgaccgatgctttggtttgggtgattgccaagagcggcatctcctcccagcagcaatccatgcgcctggct +aacctcctgatgctcctgtcccacgtcaggcatgcgagtaacaagggcatggaacatctgctcaacatgaag +tgcaaaaatgtggtcccagtgtatgacctgctgctggagatgctgaatgcccacgtgcttcgcgggtgcaag +tcctccatcacggggtccgagtgcagcccggcagaggacagtaaaagcaaagagggctcccagaacccacag +tctcag +>EMBLCDS|BAA75464/1-2547 Anguilla japonica (Japanese eel) androgen receptor alpha +atggagattccagttgggttaggaggagtttcagatgccacaaacgccgtttttcgcggaccttaccaaaac +gttttccacagccttcaagtggcatttcagagtcacggtgccgtctccaggagcttagattttccaaataca +aagtacggttttttacaaaacagacatttctgtgaaatgcgtcaggagaacaagcagccgccatgcaaagga +ctcggcctattttacgggaaccatcgtaattcggacactgggacaaacgaagacgacatcgcttgtttttcc +agacagtccgacgctgaagccagacctggtattttttctgaaagctcattggatactggagacgagattact +tgcaaactccagtcagacaaccaaggggtaagagcgagcggtcctctcctaccgggctctagcggctgcaat +tcgggacaaaagtcctcccttgcttgtacgtcccaacaaagggagacaacatctcaaagtgacacctgcgca +ggagagagctgctcggaacatcaagcaactaccatttcggaaactgcgcgcgaattgtgcaacgccgtttcc +gtgtcgctgggcttgaatttagatcttaatgatatgaatgacctaagttcaaaccaaatatcgtctaccgaa +agtgacacaagtcaagccatctacttatttgaatcttcacctgggtatactggggtcggactgaacgccttg +gtaagagactgtaaatgtcagagtgcacgcgaagggacatcgacacaacagtacgaccgcggggcaatgttt +aagataaaccgtgtaaatgacttgccgcttcagccagcacccccgcgacacaccagcattagcgatgctaaa +tgggacatggaagcaggtttgtgtgcgcagatggagcacaaagactctgaaaagtgcgcgaatatggatggt +gcacactccacttctgtcttctcccagttcgaccaactgttgccagtaaacgcgtcgcactacagtcagaac +gtttcggtcagagtggaaccacaaagtgatttctctccgattttgtacaaatcacctggtattcagaaaaat +gccgaaaagtacaatgtccaatatgatgccacaattaaatcagaagatgggaaaacgacatctgaacgggaa +tggggttttcagtacaggtacaatgaaagctgcagcacaccgtcagcacctcctagacattgtgcacatcag +aacagggccggaccgtacaaccagttcttttttaatccatttgaatatgcgaaaagaggtgttgtctcaagg +gaaggatattctctcgaacatgggttcccaaacaatctcgctcggacaccctactctggttccttgaaaaac +gaactaggagatcgtctgagtgggccataccctgacgtcagttacaggtacgagggcgagcgggagaacgtg +ttccccgtggagttcttctttccgccgcagaggacctgcctgatctgcggggacgaggcctcgggctgtcac +tatggagccctcacctgcggcagctgcaaggtgttcttcaagagggccgcggaagggaaacagaagtacctg +tgcgccagcatcaatgattgcaccattgataaacttcgaaggaagaactgcccctcttgccgtctcaaaagg +tgctttgctgccggaatgacccttggagcgcggaagctgaagaagatcgggcaaatgagggcccccgaggat +ggccaggggcagggcccggcggaagcggagctgagcgtctcccccaagtacgacctgggcttccacacccag +tccatgttcctcaacatcctggaggccatcgagccggaggtggtgaacgccgggcacgactatggccagccg +gactctgcggccagcctgctgaccagcctcaacgagctcggagaacggcaactcgtcaaggtcgtcaagtgg +gccaagggcatgccaggttttcggagtctgtacgtggatgaccagatgacagtcatccagcactcctggatg +gcagtgatggtgttcgctctgggctggaggtcatttaagaatgtgaagtccaggatgctttactttgctcct +gaccttgttttcaacgagcaccgaatgcaggtgtccaccatgtatgaacactgcatccggatgaagaacttc +tcccaggagtttgctatgctgcaggtctcccaggaagagttcctgtgcatgaaagctctgcttctcttcagc +accatccccgttgaagggctgaaggggcagaatttctttgacgagctgcggaggagctacattaacgagctg +gaccggctggttagcttcaggagcaagtccagctgttccgagaggttccagcagctcacccgcctcctggac +tccctccaacctgttctgaagaagctccaccagtttacgttcgaccttttcgtccagtcccagaacctctcc +aaccaagtttgctttcccgagatgatctcagagatcatatccgtgcacgtgccaaagattctcgctggcacg +gtgaagccaatcctcttccacaagtag +>EMBLCDS|AAK20930/1-1317 Petromyzon marinus (sea lamprey) partial corticoid receptor +ggggtggagtttcagttgccctactcggcatctgccacatcctttcgtccgtccgttgccacctcgtccgcc +tcgggcatctccaacttttcaaatgggaataattttggattcctttctcccaatggagtacaacaggatgga +tttccttaccctggtttcacgagtcccgcacagtcctcagtccctccgcagaaggcgtgtctcatctgtagt +gatgaggcttcgggctgccactacggagtgctcacctgtggaagctgcaaggtgttcttcaagcgtgccgtg +gaaggacagcacaattatctgtgcgccggacgaaacgactgcatcattgacaagatccgccgcaagaactgc +ccagcttgccgtctgcgcaagtgcatccaggctggaatgacgctaggagcacgcaagcttaagaagcaaggc +cgggtaaagggagagaaccagcgcagcccagcgtcctccacagccaccacctcgtctgccaccccgcaaccc +tccagcaactcgacggccgtgaccacgttctcgccaccgccgaccggagagcccattttctcacccacactc +atcgccatcctgcaggcgatcgagcccgaggtggtcatgtccggctatgacaacacgcggtcccagaccacc +gcctacatgctgtcgagcctcaaccgcctctgcgacaagcagctcgtgtccattgtcaagtgggccaagtct +ctgccaggtttccgaaacctgcacatcgacgaccagatggtgttaatccagtactcatggatgggcctgatg +tcatttgccatgagctggaggtccttccagcacaccaacagcaagctgctctactttgctcctgatctggtt +tttgatgagacgcgcatgcagcartcggcgatgtatcaattgtgcgtggaaatgaggcaagtctcggaggac +ttcatgaagttgcaagtcacttcagaggagtttctgtgcatgaaagccatcttgctcctgagtactgtccca +caagagggtctgaagagccagggctgcttcgaggagatgcggatcagctacatccgggaattgaaccggacc +atcgcgcggacggagaagaatgccgtgcagtgttggcagcgcttctaccagctcaccaagctgctggrctgc +atgcaggatctcgtgagcaagctcctggagttctgcttcgcaaccttcacgcagacgcaggtgtggagtgtg +gagtttcctgacatgatggccgagatcatcagtgcgcagcttgcctcgcatcatggccgagaagcccgggca +ctccacttccacaagaaatga +>EMBLCDS|AAA17402/1-1032 Serinus canaria (common canary) partial androgen receptor +gaagcctccgggtgccactacggagccctgacgtgtgggagctgcaaagtgttcttcaaacgggcagctgaa +ggtaaacagaagtacctctgtgccagccgcaacgactgcaccatcgacaagttccggcggaaaaactgcccc +tcctgccgcctgcgcaagtgctacgaggccgggatgacgcttggagcccgcaagctgaagaaactgggtaac +ctgaaggcacaggacgacatagagggagccagctcgtccagcccaacggaggagcaagctcccaagctggtg +atgacacgcattgatggctacgagtgccagcccatcttcctcaacgtcctggaggccatcgagcctggggtg +gtgtgtgctggccatgacaacagccagcctgactccttctccaacctgctgaccagcctgaatgagcttggg +gagaggcagctggtctacgtggtcaaatgggcaaaggctctgccaggatttcgcaacctgcatgtggatgac +cagatgtcaataatccagtactcttggatgggcctgatggtgtttgctatggggtggagatccttcaccaac +gtcaattccaggatgctttactttgctccagacctggtcttcaatgagtaccgcatgcacaaatccaggatg +tacagccagtgcatcaggatgcggcacctctcccaggaattcgggtggcttcagatcacaccccaggggttc +ctctgtatgaaggctctcctcttcttcagtattattccagtggatggcctgaagaaccagaagctcttcgat +gagctccgcatgaattacatcaaggaacttgaccgtatcattgcctgcaagaggaagaaccccacctcatgc +tcccggaggttttaccagctcaccaaggtcctggactccgtgactccgattgccaaggacctgcatcagttt +acatttgatctcctaatcaaggcacacatggtgagcgtggactacccagaaatgatggctgagatcatctct +gtgcaggttcccaagatcctgtct +>EMBLCDS|AAL37553/1-1455 Drosophila melanogaster (fruit fly) estrogen-related receptor +atgtccgacggcgtcagcatcttgcacatcaaacaggaggtggacactccatcggcgtcctgctttagtccc +agctccaagtcaacggccacgcagagtggcacaaacggcctgaaatcctcgccctcggtttcgccggaaagg +cagctctgcagctcgacgacctctctatcctgcgatttgcacaatgtatccttaagcaatgatggcgatagt +ctgaaaggaagtggtacaagtggcggcaatggcggaggaggaggtggtggtacgagtggtggaaatgcgacc +aatgcgagtgccggagctggatcgggatccgtcagggacgagctccgccgattgtgtttggtttgtggcgat +gtggccagtggattccactatggtgtggcgagttgtgaggcttgcaaagcgttctttaaacgcaccatccaa +ggcaacatcgagtacacgtgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgccaa +gcgtgtcgcttccagaaatgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgtgga +ggacggcagaagtaccgaaggaatcctgtatcaaactcttaccagactatgcagctgctataccaatccaac +accacctcgctgtgcgatgtcaagatactggaggtgctcaattcatatgagccggatgccttgagcgtccaa +acgccgccgccgcaagtccacacgactagcataactaatgatgaggcctcatcctcctcgggcagcataaaa +ctggagtccagcgttgttacgcccaatgggacttgcattttccaaaacaacaacaacaatgatcccaatgag +atactaagcgtccttagtgatatttacgacaaggaattggtcagcgtcattggctgggccaagcagatacct +ggctttatagatctgccacttaacgaccagatgaagcttctccaggtgtcgtgggcagagatcctgacgctc +cagctgaccttccggtccctaccgttcaatggcaagttatgcttcgccacggatgtctggatggatgaacat +ttggccaaggagtgcggttacacggagttctactaccactgcgtccagatcgcacagcgcatggaaagaata +tcgccacgaagggaggagtactacttgctaaaggcgctcctgctggccaactgcgacattctgctggatgat +cagagttccctgcgcgcatttcgtgatacgattcttaattctctaaacgatgtggtctacttgctgcgtcat +tcgtcggccgtgtcgcatcagcaacaattgctgcttttgctgccttcgctgcggcaggcggatgatatcctg +cgaagattttggcgtggaattgcacgcgatgaagtcattaccatgaagaaactgttcctcgagatgctcgag +ccgctggccaggtga +>EMBLCDS|AAK20929/1-1662 Petromyzon marinus (sea lamprey) partial estrogen receptor +gcacgaggcttcagcgaggcacatggctacgagtactccggggcctcgctctaccagccactgcctccctcg +tgcacagagttctcaattggagctcatcaacaacaacaacatcagcaccagcatcaccagcaccagcatcag +cagcaccaccaccagcagcagcagcagcagccacagccgcagcagaatggagttttgggcgaggggcagagt +tcccatctctcttatcttccgccctcgaccgagctgccccagtacgtgccctccagccccagcgcgccctac +agcatggagctcggggcagggcgtcctcacggctacgacccagggccacagagcctctacaggggcggtgtg +gagagcagcgcccccccgtacagcgagcagcagcaggtggtgggcggcggcggagccatgtcggccatgggc +ttgacagagccacgccacgtcagctccggatcgctacccagcagcacgaggcccgagcgcagcacccagttc +tgtgccgtgtgcagcgactatgcctcggggtaccactacggcgtgtggtcctgcgagggctgcaaagccttc +ttcaagcgcagcacgcaaggccacaatgactacatgtgcccggccaccaaccagtgcaccatcgacaggaac +cgtcgcaagagctgtcaggcttgccgcctgcgtaagtgctacgaagtgggcatggtcaaaggcgttcgcaag +gaccgcaaaggctttcgaggggtcaagcacaaacgtaagcgccccatcccccaaaagaatgggggagaagga +ggtgccggcggcggccaagacgtgagcgagacgaggcctcagggtgagaggccctccgggccgagggaccgg +gagagcgccgtcagctcactcgaggctgaccaggtgatctcggctcttctggaggctgagccacccaccgta +ctgtcctcgtatgaccccgacaagcctgtgacggaggcctcgctcatggctgctctcaccagcctggctgac +cgagagctcgtgcacatgatcacctgggctaagaagattccaggattcacggccatcgggctgagtgaccag +gtgcagctgctggagtgctgctggctggagatcctaatcgtggggctcatctggaggtctatcgatcgccct +ggtcagctccactttgctccaaacctcatcctaggaagggaggacgcgcgcaatgtggagggcatgctggac +atgttcgacatgctgctcgtcaccgtgagtcgcttccgtgagctgcatctccgccgggaggaatacgtctgc +ctcaaggccatgatcctcctcaactcgggggtgtttttctgcctctccaattccgccggggagcagacgaat +gtgcagctcatccagcagatcctcgagaaggtgatggacgccctgggcagcaccatcggccacattgaggcg +tccccgccgcaacactcgcgtcgcctctcccagctgctcctgctgctttcacagatccggcacattagcaac +aagggcatcgagcatctcaacagcatgaagcgtaagaatgtgatcccgctatacgacctgctccttgagctg +ctggacgctcacagcctgcagaatactggcttacggacgtcgcccccaccgcaggatttcagggcaaccctc +gtgccg diff --git a/examples/estrogenReceptorProtein.fa b/examples/estrogenReceptorProtein.fa new file mode 100644 index 0000000..0541d39 --- /dev/null +++ b/examples/estrogenReceptorProtein.fa @@ -0,0 +1,81 @@ +>UNIPROT|Q7LCB3/1-530 estrogen nuclear receptor beta variant a +MDIKNSPSSLNSPSSYNCSQSILPLEHGSIYIPSSYVDSHHEYPAMTFYSPAVMNYSIPSNVTNLEGGPGRQ +TTSPNVLWPTPGHLSPLVVHRQLSHLYAEPQKSPWCEARSLEHTLPVNRETLKRKVSGNRCASPVTGPGSKR +DAHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVK +CGSRRERCGYRLVRRQRSADEQLHCAGKAKRSGGHAPRVRELLLDALSPEQLVLTLLEAEPPHVLISRPSAP +FTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDL +VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNA +VTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVLRGCK +SSITGSECSPAEDSKSKEGSQNPQSQ +>UNIPROT|Q9VSE9/1-484 GH28308p +MSDGVSILHIKQEVDTPSASCFSPSSKSTATQSGTNGLKSSPSVSPERQLCSSTTSLSCDLHNVSLSNDGDS +LKGSGTSGGNGGGGGGGTSGGNATNASAGAGSGSVRDELRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ +GNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSYQTMQLLYQSN +TTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSIKLESSVVTPNGTCIFQNNNNNDPNE +ILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQVSWAEILTLQLTFRSLPFNGKLCFATDVWMDEH +LAKECGYTEFYYHCVQIAQRMERISPRREEYYLLKALLLANCDILLDDQSSLRAFRDTILNSLNDVVYLLRH +SSAVSHQQQLLLLLPSLRQADDILRRFWRGIARDEVITMKKLFLEMLEPLAR +>UNIPROT|Q9IBD5/1-710 progesterone receptor +MDNNHQDKMESLYTPARASPTPDAESIKRARNLIKTYSESFGSYVEEIVRDDSNNIQSLSSVPLLMRNFGNM +DTLTCAPGSGSDSEIWKDFVVPGNSVVSKDTCGHVEISTKAENLSWAAAPLSREETLAKGTVTVPATVPKES +FTATSNTSSASGISIKDEQQSLLKMEPQSSDFCPYTANIPKLNPSYLTNTASTKQLGYGEQPDTSAHSSPPA +QKIVLDTARYSADLCSDNPLPQATNIKTDPCSSFSSFVGEGILTRASMGYSQQAIQTLPVHKSEPFRLSASS +APADSPFWCQSTGPSEDHHLQIDYLSPAGLHSTCKYSSTNAYSSYLGVLPQRVCVICGDEASGCHYGVLTCG +SCKVFFKRAVEGHHNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMILGGRKLKKLGALKAAGLTQALVAH +SLTPRRLSGDSQALMPLGCLPGVRELHLSPQIISVLESIEPEVVYSGYDNSQPDMPNMLLNSLNRLCERQLL +RIVKWSKSLPGFRSLHINDQMALIQYSWMSLMVFSLGWRSFQNVTSDYLYFAPDLILNEEYMRRSPIFDLCM +AMQFIPQEFANLQVTKEEFLCMKVLLLLNTVPLEGLKSQPQFDEMRQNYIHELTKAIHLRENGVVACSQRFY +HLTKLMDHMHDIVKKLHLYCLSTFIQADAMRVEFPEMMSEVIASQLPRVLAGMVKPLLFHTK +>UNIPROT|Q7LCB3/1-530 estrogen receptor 2 isoform A +MDIKNSPSSLNSPSSYNCSQSILPLEHGSIYIPSSYVDSHHEYPAMTFYSPAVMNYSIPSNVTNLEGGPGRQ +TTSPNVLWPTPGHLSPLVVHRQLSHLYAEPQKSPWCEARSLEHTLPVNRETLKRKVSGNRCASPVTGPGSKR +DAHFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVK +CGSRRERCGYRLVRRQRSADEQLHCAGKAKRSGGHAPRVRELLLDALSPEQLVLTLLEAEPPHVLISRPSAP +FTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDL +VLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNA +VTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVLRGCK +SSITGSECSPAEDSKSKEGSQNPQSQ +>UNIPROT|Q9YGV9/1-848 androgen receptor alpha +MEIPVGLGGVSDATNAVFRGPYQNVFHSLQVAFQSHGAVSRSLDFPNTKYGFLQNRHFCEMRQENKQPPCKG +LGLFYGNHRNSDTGTNEDDIACFSRQSDAEARPGIFSESSLDTGDEITCKLQSDNQGVRASGPLLPGSSGCN +SGQKSSLACTSQQRETTSQSDTCAGESCSEHQATTISETARELCNAVSVSLGLNLDLNDMNDLSSNQISSTE +SDTSQAIYLFESSPGYTGVGLNALVRDCKCQSAREGTSTQQYDRGAMFKINRVNDLPLQPAPPRHTSISDAK +WDMEAGLCAQMEHKDSEKCANMDGAHSTSVFSQFDQLLPVNASHYSQNVSVRVEPQSDFSPILYKSPGIQKN +AEKYNVQYDATIKSEDGKTTSEREWGFQYRYNESCSTPSAPPRHCAHQNRAGPYNQFFFNPFEYAKRGVVSR +EGYSLEHGFPNNLARTPYSGSLKNELGDRLSGPYPDVSYRYEGERENVFPVEFFFPPQRTCLICGDEASGCH +YGALTCGSCKVFFKRAAEGKQKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMTLGARKLKKIGQMRAPED +GQGQGPAEAELSVSPKYDLGFHTQSMFLNILEAIEPEVVNAGHDYGQPDSAASLLTSLNELGERQLVKVVKW +AKGMPGFRSLYVDDQMTVIQHSWMAVMVFALGWRSFKNVKSRMLYFAPDLVFNEHRMQVSTMYEHCIRMKNF +SQEFAMLQVSQEEFLCMKALLLFSTIPVEGLKGQNFFDELRRSYINELDRLVSFRSKSSCSERFQQLTRLLD +SLQPVLKKLHQFTFDLFVQSQNLSNQVCFPEMISEIISVHVPKILAGTVKPILFHK +>UNIPROT|Q90ZM7/1-438 corticoid receptor +GVEFQLPYSASATSFRPSVATSSASGISNFSNGNNFGFLSPNGVQQDGFPYPGFTSPAQSSVPPQKACLICS +DEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCIQAGMTLGARKLKKQG +RVKGENQRSPASSTATTSSATPQPSSNSTAVTTFSPPPTGEPIFSPTLIAILQAIEPEVVMSGYDNTRSQTT +AYMLSSLNRLCDKQLVSIVKWAKSLPGFRNLHIDDQMVLIQYSWMGLMSFAMSWRSFQHTNSKLLYFAPDLV +FDETRMQQSAMYQLCVEMRQVSEDFMKLQVTSEEFLCMKAILLLSTVPQEGLKSQGCFEEMRISYIRELNRT +IARTEKNAVQCWQRFYQLTKLLXCMQDLVSKLLEFCFATFTQTQVWSVEFPDMMAEIISAQLASHHGREARA +LHFHKK +>UNIPROT|Q91445/1-344 androgen receptor +EASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLGN +LKAQDDIEGASSSSPTEEQAPKLVMTRIDGYECQPIFLNVLEAIEPGVVCAGHDNSQPDSFSNLLTSLNELG +ERQLVYVVKWAKALPGFRNLHVDDQMSIIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRM +YSQCIRMRHLSQEFGWLQITPQGFLCMKALLFFSIIPVDGLKNQKLFDELRMNYIKELDRIIACKRKNPTSC +SRRFYQLTKVLDSVTPIAKDLHQFTFDLLIKAHMVSVDYPEMMAEIISVQVPKILS +>UNIPROT|Q9VSE9/1-484 estrogen-related receptor +MSDGVSILHIKQEVDTPSASCFSPSSKSTATQSGTNGLKSSPSVSPERQLCSSTTSLSCDLHNVSLSNDGDS +LKGSGTSGGNGGGGGGGTSGGNATNASAGAGSGSVRDELRRLCLVCGDVASGFHYGVASCEACKAFFKRTIQ +GNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSYQTMQLLYQSN +TTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSIKLESSVVTPNGTCIFQNNNNNDPNE +ILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQVSWAEILTLQLTFRSLPFNGKLCFATDVWMDEH +LAKECGYTEFYYHCVQIAQRMERISPRREEYYLLKALLLANCDILLDDQSSLRAFRDTILNSLNDVVYLLRH +SSAVSHQQQLLLLLPSLRQADDILRRFWRGIARDEVITMKKLFLEMLEPLAR +>UNIPROT|Q90ZM8/1-554 estrogen receptor +ARGFSEAHGYEYSGASLYQPLPPSCTEFSIGAHQQQQHQHQHHQHQHQQHHHQQQQQQPQPQQNGVLGEGQS +SHLSYLPPSTELPQYVPSSPSAPYSMELGAGRPHGYDPGPQSLYRGGVESSAPPYSEQQQVVGGGGAMSAMG +LTEPRHVSSGSLPSSTRPERSTQFCAVCSDYASGYHYGVWSCEGCKAFFKRSTQGHNDYMCPATNQCTIDRN +RRKSCQACRLRKCYEVGMVKGVRKDRKGFRGVKHKRKRPIPQKNGGEGGAGGGQDVSETRPQGERPSGPRDR +ESAVSSLEADQVISALLEAEPPTVLSSYDPDKPVTEASLMAALTSLADRELVHMITWAKKIPGFTAIGLSDQ +VQLLECCWLEILIVGLIWRSIDRPGQLHFAPNLILGREDARNVEGMLDMFDMLLVTVSRFRELHLRREEYVC +LKAMILLNSGVFFCLSNSAGEQTNVQLIQQILEKVMDALGSTIGHIEASPPQHSRRLSQLLLLLSQIRHISN +KGIEHLNSMKRKNVIPLYDLLLELLDAHSLQNTGLRTSPPPQDFRATLVP -- 1.7.10.2