JAL-1684 aligned proteins and citation for for Estrogen cDNA/Protein

diff --git a/examples/applets.html b/examples/applets.html
index a101d65..ff97475 100644 (file)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -168,7 +168,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
     </tr>
   </table>
   <p>
-    <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
+    <h2>Linked Protein and cDNA alignments for a family of Steroid Receptors</h2>
   </p>
   <table width="90%">
     <tr>
@@ -191,6 +191,11 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
      value="http://www.jalview.org/services/launchApp"/>
 </applet>
 </td>
-      <td valign="center">Displays a split window view of protein and its related cDNA</td>
+      <td valign="center">Displays a split window view of protein
+        and its related cDNA.<br />Data retrieved from Uniprot and ENA,
+        after Thornton, Need and Crews, <a
+        href="http://dx.doi.org/10.1126/science.1086185">Science 19
+          September 2003: 301 (5640), 1714-1717</a>
+      </td>
     </tr>
   </table>

diff --git a/examples/estrogenReceptorProtein.aln b/examples/estrogenReceptorProtein.aln
new file mode 100644 (file)
index 0000000..cfe7d80
--- /dev/null
+++ b/examples/estrogenReceptorProtein.aln
@@ -0,0 +1,162 @@
+CLUSTAL
+
+UNIPROT|Q7LCB3/1-530 -------MDIKNSPSSLNSPSSYNCSQSILPLEHG-----------SIYIPSSYVDSHHE
+UNIPROT|Q9VSE9/1-484 ----------------------------------M-----------SDGVSILHIKQEVD
+UNIPROT|Q9IBD5/1-710 -----MDNNHQDKMESLYTPARASPTPDAESIKRARNLIKTYSESFGSYVEEIVRDDSNN
+UNIPROT|Q7LCB3/1-530 -------MDIKNSPSSLNSPSSYNCSQSILPLEHG-----------SIYIPSSYVDSHHE
+UNIPROT|Q9YGV9/1-848 MEIPVGLGGVSDATNAVFRGPYQNVFHSLQ----------------VAFQSHGAVSRSLD
+UNIPROT|Q90ZM7/1-438 -----------------------------------------------------GVEFQLP
+UNIPROT|Q91445/1-344 ------------------------------------------------------------
+UNIPROT|Q9VSE9/1-484 ----------------------------------M-----------SDGVSILHIKQEVD
+UNIPROT|Q90ZM8/1-554 ARGFSEAHGYEYSGASLYQPLPPSCTEFSI----------------GAHQQQQHQHQHHQ
+
+UNIPROT|Q7LCB3/1-530 YPAM--------------------------------------------TFYSPAVMNYSI
+UNIPROT|Q9VSE9/1-484 TPSA--------------------------------------------SCFSPSSKSTAT
+UNIPROT|Q9IBD5/1-710 IQSLSSVPLLMRNFGNMDTLTCAPGSGSDSEIWKDFVVPGNSVVSKD-TCGHVEISTKAE
+UNIPROT|Q7LCB3/1-530 YPAM--------------------------------------------TFYSPAVMNYSI
+UNIPROT|Q9YGV9/1-848 FPNTKYGFLQNRHFCEMRQENKQPPCKGLGLFYGNHRNSDTGTNEDDIACFSRQSDAEAR
+UNIPROT|Q90ZM7/1-438 YSASA-------------------------------------------TSFRPSVATSSA
+UNIPROT|Q91445/1-344 ------------------------------------------------------------
+UNIPROT|Q9VSE9/1-484 TPSA--------------------------------------------SCFSPSSKSTAT
+UNIPROT|Q90ZM8/1-554 HQHQ--------------------------------------------QHHHQQQQQQPQ
+
+UNIPROT|Q7LCB3/1-530 P---------SNVTNLEGGP-------GRQTTSPNVLWPTPGHLSPLVVHRQLSHLYAEP
+UNIPROT|Q9VSE9/1-484 Q---------SGTNGLKSSP----------SVSPERQLCSS--TTSLSCDLHNVSLSNDG
+UNIPROT|Q9IBD5/1-710 NLSWAAAPL-SREETLAKGTVTVPATVPKESFTATSNTSSASGIS--IKDEQQSLLKMEP
+UNIPROT|Q7LCB3/1-530 P---------SNVTNLEGGP-------GRQTTSPNVLWPTPGHLSPLVVHRQLSHLYAEP
+UNIPROT|Q9YGV9/1-848 PGIFSESSLDTGDEITCKLQSDNQGVRASGPLLPGSSGCNSGQKSSLACTSQQRETTSQS
+UNIPROT|Q90ZM7/1-438 ----------SGISNFSNGN----------------------------------------
+UNIPROT|Q91445/1-344 ------------------------------------------------------------
+UNIPROT|Q9VSE9/1-484 Q---------SGTNGLKSSP----------SVSPERQLCSS--TTSLSCDLHNVSLSNDG
+UNIPROT|Q90ZM8/1-554 P---------QQNGVLGEGQSSHLSYLPPSTELPQYVPSSPSAPYSMELGAGRPHGYDPG
+
+UNIPROT|Q7LCB3/1-530 QKSPWCE---------------------------------------------------AR
+UNIPROT|Q9VSE9/1-484 DS--------------------------------------------------------LK
+UNIPROT|Q9IBD5/1-710 QSSDFCPYTANIPKLNP-----------------------------------------SY
+UNIPROT|Q7LCB3/1-530 QKSPWCE---------------------------------------------------AR
+UNIPROT|Q9YGV9/1-848 DTCAGESCSEHQATTISETARELCNAVSVSLGLNLDLNDMNDLSSNQISSTESDTSQAIY
+UNIPROT|Q90ZM7/1-438 ----------------------------------------------------------NF
+UNIPROT|Q91445/1-344 ------------------------------------------------------------
+UNIPROT|Q9VSE9/1-484 DS--------------------------------------------------------LK
+UNIPROT|Q90ZM8/1-554 PQSLYRGGVE------------------------------------------------SS
+
+UNIPROT|Q7LCB3/1-530 SLEHTLPVNRETLKRKVSGNRCASPV----------------------------------
+UNIPROT|Q9VSE9/1-484 GSGTSGGNGGGGGGGTSGGNATNASA----------------------------------
+UNIPROT|Q9IBD5/1-710 LTNTASTKQLGYGEQPDTSAHSSPPA----------------------------------
+UNIPROT|Q7LCB3/1-530 SLEHTLPVNRETLKRKVSGNRCASPV----------------------------------
+UNIPROT|Q9YGV9/1-848 LFESSPGYTGVGLNALVRDCKCQSAREGTSTQQYDRGAMFKINRVNDLPLQPAPPRHTSI
+UNIPROT|Q90ZM7/1-438 GFLSPNGVQQDGFPYPGFTSPAQSSV----------------------------------
+UNIPROT|Q91445/1-344 ------------------------------------------------------------
+UNIPROT|Q9VSE9/1-484 GSGTSGGNGGGGGGGTSGGNATNASA----------------------------------
+UNIPROT|Q90ZM8/1-554 APPYSEQQQVVGGGGAMSAMGLTEPR----------------------------------
+
+UNIPROT|Q7LCB3/1-530 ------------------------------------------------------------
+UNIPROT|Q9VSE9/1-484 ------------------------------------------------------------
+UNIPROT|Q9IBD5/1-710 QKIVLDTARYSADLCSDNPLPQATNIKTDPCSSFSSFVGEGILTRASMGYSQQAIQTLPV
+UNIPROT|Q7LCB3/1-530 ------------------------------------------------------------
+UNIPROT|Q9YGV9/1-848 SDAKWDMEAGLCAQMEHKDSEKCANMDGAHSTSVFSQFDQLLPVNASHYSQNVSVRVEPQ
+UNIPROT|Q90ZM7/1-438 ------------------------------------------------------------
+UNIPROT|Q91445/1-344 ------------------------------------------------------------
+UNIPROT|Q9VSE9/1-484 ------------------------------------------------------------
+UNIPROT|Q90ZM8/1-554 ------------------------------------------------------------
+
+UNIPROT|Q7LCB3/1-530 ------------------------------------------------------------
+UNIPROT|Q9VSE9/1-484 ------------------------------------------------------------
+UNIPROT|Q9IBD5/1-710 HKSEPFRLSASSAPADSPFW----------------------------------------
+UNIPROT|Q7LCB3/1-530 ------------------------------------------------------------
+UNIPROT|Q9YGV9/1-848 SDFSPILYKSPGIQKNAEKYNVQYDATIKSEDGKTTSEREWGFQYRYNESCSTPSAPPRH
+UNIPROT|Q90ZM7/1-438 ------------------------------------------------------------
+UNIPROT|Q91445/1-344 ------------------------------------------------------------
+UNIPROT|Q9VSE9/1-484 ------------------------------------------------------------
+UNIPROT|Q90ZM8/1-554 ------------------------------------------------------------
+
+UNIPROT|Q7LCB3/1-530 --------------------------------------------TGPGSKRDA-------
+UNIPROT|Q9VSE9/1-484 -------------------------------------------GAGSGSVRDELR-----
+UNIPROT|Q9IBD5/1-710 -------------------------------------------CQSTGPSEDHHLQIDYL
+UNIPROT|Q7LCB3/1-530 --------------------------------------------TGPGSKRDA-------
+UNIPROT|Q9YGV9/1-848 CAHQNRAGPYNQFFFNPFEYAKRGVVSREGYSLEHGFPNNLARTPYSGSLKNELGDRLSG
+UNIPROT|Q90ZM7/1-438 ------------------------------------------------------------
+UNIPROT|Q91445/1-344 ------------------------------------------------------------
+UNIPROT|Q9VSE9/1-484 -------------------------------------------GAGSGSVRDELR-----
+UNIPROT|Q90ZM8/1-554 -------------------------------------------HVSSGSLPSSTRPE---
+
+UNIPROT|Q7LCB3/1-530 --------------------------HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGH
+UNIPROT|Q9VSE9/1-484 --------------------------RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGN
+UNIPROT|Q9IBD5/1-710 SPAGLHSTCKYSSTNAYSSYLGVLPQRVCVICGDEASGCHYGVLTCGSCKVFFKRAVEGH
+UNIPROT|Q7LCB3/1-530 --------------------------HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGH
+UNIPROT|Q9YGV9/1-848 PYPDVSYRYEGERENVFPVEFFFPPQRTCLICGDEASGCHYGALTCGSCKVFFKRAAEGK
+UNIPROT|Q90ZM7/1-438 -----------------------PPQKACLICSDEASGCHYGVLTCGSCKVFFKRAVEGQ
+UNIPROT|Q91445/1-344 ----------------------------------EASGCHYGALTCGSCKVFFKRAAEGK
+UNIPROT|Q9VSE9/1-484 --------------------------RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGN
+UNIPROT|Q90ZM8/1-554 -----------------------RSTQFCAVCSDYASGYHYGVWSCEGCKAFFKRSTQGH
+
+UNIPROT|Q7LCB3/1-530 NDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRER-CGYRLVRRQRSADEQL
+UNIPROT|Q9VSE9/1-484 IEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSY
+UNIPROT|Q9IBD5/1-710 HNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMI---------LGGRKLKKLGALKAAG
+UNIPROT|Q7LCB3/1-530 NDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRER-CGYRLVRRQRSADEQL
+UNIPROT|Q9YGV9/1-848 QKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMT---------LGARKLKKIGQMRAPE
+UNIPROT|Q90ZM7/1-438 HNYLCAGRNDCIIDKIRRKNCPACRLRKCIQAGMT---------LGARKLKKQGRVKGEN
+UNIPROT|Q91445/1-344 QKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMT---------LGARKLKKLGNLKAQD
+UNIPROT|Q9VSE9/1-484 IEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSY
+UNIPROT|Q90ZM8/1-554 NDYMCPATNQCTIDRNRRKSCQACRLRKCYEVGMVK-GVRKDR-KGFRGVKHKRKRPIPQ
+
+UNIPROT|Q7LCB3/1-530 HCAGKAKRSGGH------------------------APRVRELLLDALSPE--------Q
+UNIPROT|Q9VSE9/1-484 QTMQLLYQSNTTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSI--K
+UNIPROT|Q9IBD5/1-710 LTQALVAHSLTPRR---------LSGDSQALMPLGCLPGVRELHLS-------------P
+UNIPROT|Q7LCB3/1-530 HCAGKAKRSGGH------------------------APRVRELLLDALSPE--------Q
+UNIPROT|Q9YGV9/1-848 DGQGQGPAEAELSV----------------------SPKYDLGFHTQ------------S
+UNIPROT|Q90ZM7/1-438 QRSPASSTATTSSA--------------------TPQPSSNSTAVTTFSPPPTGEPIFSP
+UNIPROT|Q91445/1-344 DIEGASSSSPTEEQ----------------------APKLVMTRIDGYECQ--------P
+UNIPROT|Q9VSE9/1-484 QTMQLLYQSNTTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSI--K
+UNIPROT|Q90ZM8/1-554 KNGGEGGAGGGQDV-----------SETRPQGERPSGPRDRESAVSSLEAD--------Q
+
+UNIPROT|Q7LCB3/1-530 LVLTLLEA-EPPHVLISR-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLF
+UNIPROT|Q9VSE9/1-484 LESSVVTP-NGTCIFQNNNNNDP---NEILSVLSDIYDKELVSVIGWAKQIPGFIDLPLN
+UNIPROT|Q9IBD5/1-710 QIISVLESIEPEVVYSGYDNSQPDMPNMLLNSLNRLCERQLLRIVKWSKSLPGFRSLHIN
+UNIPROT|Q7LCB3/1-530 LVLTLLEA-EPPHVLISR-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLF
+UNIPROT|Q9YGV9/1-848 MFLNILEAIEPEVVNAGHDYGQPDSAASLLTSLNELGERQLVKVVKWAKGMPGFRSLYVD
+UNIPROT|Q90ZM7/1-438 TLIAILQAIEPEVVMSGYDNTRSQTTAYMLSSLNRLCDKQLVSIVKWAKSLPGFRNLHID
+UNIPROT|Q91445/1-344 IFLNVLEAIEPGVVCAGHDNSQPDSFSNLLTSLNELGERQLVYVVKWAKALPGFRNLHVD
+UNIPROT|Q9VSE9/1-484 LESSVVTP-NGTCIFQNNNNNDP---NEILSVLSDIYDKELVSVIGWAKQIPGFIDLPLN
+UNIPROT|Q90ZM8/1-554 VISALLEA-EPPTVLSSYDPDKPVTEASLMAALTSLADRELVHMITWAKKIPGFTAIGLS
+
+UNIPROT|Q7LCB3/1-530 DQVRLLESCWMEVLMMGLMWRSIDH--PGKLIFAPDLVLDRDEGKCVEGILEIFDMLLA-
+UNIPROT|Q9VSE9/1-484 DQMKLLQVSWAEILTLQLTFRSLPF--NGKLCFATDVWMDEHLAKEC-GYTEFYYHCVQ-
+UNIPROT|Q9IBD5/1-710 DQMALIQYSWMSLMVFSLGWRSFQNVTSDYLYFAPDLILNEEYMRRS----PIFDLCMAM
+UNIPROT|Q7LCB3/1-530 DQVRLLESCWMEVLMMGLMWRSIDH--PGKLIFAPDLVLDRDEGKCVEGILEIFDMLLA-
+UNIPROT|Q9YGV9/1-848 DQMTVIQHSWMAVMVFALGWRSFKNVKSRMLYFAPDLVFNEHRMQVS----TMYEHCIRM
+UNIPROT|Q90ZM7/1-438 DQMVLIQYSWMGLMSFAMSWRSFQHTNSKLLYFAPDLVFDETRMQQS----AMYQLCVEM
+UNIPROT|Q91445/1-344 DQMSIIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKS----RMYSQCIRM
+UNIPROT|Q9VSE9/1-484 DQMKLLQVSWAEILTLQLTFRSLPF--NGKLCFATDVWMDEHLAKEC-GYTEFYYHCVQ-
+UNIPROT|Q90ZM8/1-554 DQVQLLECCWLEILIVGLIWRSIDR--PGQLHFAPNLILGREDARNVEGMLDMFDMLLV-
+
+UNIPROT|Q7LCB3/1-530 --TTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKL-AHLLNAVTDALVW
+UNIPROT|Q9VSE9/1-484 --IAQRMERISPRREEYYLLKALLLANC------DILLDDQSSLRAFRDTILNSLNDVVY
+UNIPROT|Q9IBD5/1-710 QFIPQEFANLQVTKEEFLCMKVLLLLN-------TVPLEGLKSQPQFDEMRQNYIHELTK
+UNIPROT|Q7LCB3/1-530 --TTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKL-AHLLNAVTDALVW
+UNIPROT|Q9YGV9/1-848 KNFSQEFAMLQVSQEEFLCMKALLLFS-------TIPVEGLKGQNFFDELRRSYINELDR
+UNIPROT|Q90ZM7/1-438 RQVSEDFMKLQVTSEEFLCMKAILLLS-------TVPQEGLKSQGCFEEMRISYIRELNR
+UNIPROT|Q91445/1-344 RHLSQEFGWLQITPQGFLCMKALLFFS-------IIPVDGLKNQKLFDELRMNYIKELDR
+UNIPROT|Q9VSE9/1-484 --IAQRMERISPRREEYYLLKALLLANC------DILLDDQSSLRAFRDTILNSLNDVVY
+UNIPROT|Q90ZM8/1-554 --TVSRFRELHLRREEYVCLKAMILLNSGVFFCLSNSAGEQTNVQLIQQILEKVMDALGS
+
+UNIPROT|Q7LCB3/1-530 VIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNV-----VPVYDLLLEM
+UNIPROT|Q9VSE9/1-484 LLRHSSAVSHQQ-----QLLLLLPSLRQADDILRRFWRGIARDEV-----ITMKKLFLEM
+UNIPROT|Q9IBD5/1-710 AIHLRENGVVACSQRFYHLTKLMDHMHDIVKKLHLYCLSTFIQADAMR--VEFPEMMSEV
+UNIPROT|Q7LCB3/1-530 VIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNV-----VPVYDLLLEM
+UNIPROT|Q9YGV9/1-848 LVSFRSK--SSCSERFQQLTRLLDSLQPVLKKLHQFTFDLFVQSQNLSNQVCFPEMISEI
+UNIPROT|Q90ZM7/1-438 TIARTEKNAVQCWQRFYQLTKLLXCMQDLVSKLLEFCFATFTQTQVWS--VEFPDMMAEI
+UNIPROT|Q91445/1-344 IIACKRKNPTSCSRRFYQLTKVLDSVTPIAKDLHQFTFDLLIKAHMVS--VDYPEMMAEI
+UNIPROT|Q9VSE9/1-484 LLRHSSAVSHQQ-----QLLLLLPSLRQADDILRRFWRGIARDEV-----ITMKKLFLEM
+UNIPROT|Q90ZM8/1-554 TIGHIEASPPQHSRRLSQLLLLLSQIRHISNKGIEHLNSMKRKNV-----IPLYDLLLEL
+
+UNIPROT|Q7LCB3/1-530 LNAHVLRGCKSSITGSECSPAEDSKSKEGSQNPQSQ---
+UNIPROT|Q9VSE9/1-484 LE------------------------------PLAR---
+UNIPROT|Q9IBD5/1-710 IASQL------------------PRVLAGMVKPLLFHTK
+UNIPROT|Q7LCB3/1-530 LNAHVLRGCKSSITGSECSPAEDSKSKEGSQNPQSQ---
+UNIPROT|Q9YGV9/1-848 ISVHV------------------PKILAGTVKPILFHK-
+UNIPROT|Q90ZM7/1-438 ISAQL------------------ASHHGREARALHFHKK
+UNIPROT|Q91445/1-344 ISVQV------------------PKILS-----------
+UNIPROT|Q9VSE9/1-484 LE------------------------------PLAR---
+UNIPROT|Q90ZM8/1-554 LDAHSLQN-----TGLRTSPP--PQDFRATLVP------
+