JAL-1684 applet example for SplitFrame view of cDNA/Protein

diff --git a/examples-jbake/templates/jvl_examples.ftl b/examples-jbake/templates/jvl_examples.ftl
index f2bf8b1..d5e328e 100644 (file)
--- 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.<br/>
        secondary structure annotation</td>
     </tr>
   </table>
+  <p>
+    <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
+  </p>
+  <table width="90%">
+    <tr>
+      <td width="10%" valign="center"><@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 /></td>
+      <td valign="center">Displays a split window view of protein and its related cDNA</td>
+    </tr>
+  </table>
 </div>

diff --git a/examples/applets.html b/examples/applets.html
index cc85e86..7044253 100755 (executable)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -313,6 +313,29 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
        secondary structure annotation</td>
     </tr>
   </table>
+  <p>
+    <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
+  </p>
+  <table width="90%">
+    <tr>
+      <td width="10%" valign="center"><applet
+   code="jalview.bin.JalviewLite" width="140" height="35"
+   archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox"/>
+<param name="file" value="estrogenReceptorCdna.fa"/>
+<param name="file" value="estrogenReceptorProtein.fa"/>
+<param name="showFullId" value="false"/>
+<param name="windowHeight" value="800"/>
+<param name="windowWidth" value="650"/>
+<param name="showAnnotation" value="true"/>
+<param name="defaultColour" value="Purine/Pyrimidine"/>
+   <param name="APPLICATION_URL"
+     value="http://www.jalview.org/services/launchApp"/>
+</applet>
+</td>
+      <td valign="center">Displays a split window view of protein and its related cDNA</td>
+    </tr>
+  </table>
 </div>
 <!-- content template end -->
 

diff --git a/examples/estrogenReceptorCdna.fa b/examples/estrogenReceptorCdna.fa
new file mode 100644 (file)
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 (file)
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