Dear Developers
I would like to visualize the secondary structure of a sequence alignment.
But there is something wrong in my code.
can you help me?
Thanks in advance and best regards,
Matteo Floris
These are the sequences (file TMP/4e28253ce1ab5.fasta)
>P30543
MGSSVYITVELAIAVLAILGNVLVCWAVWINSNLQNVTNFFVVSLAAADIAVGVLAIPFA
ITISTGFCAACHGCLFFACFVLVLTQSSIFSLLAIAIDRYIAIRIPLRYNGLVTGVRAKG
IIAICWVLSFAIGLTPMLGWNNCSQKDG--NSTKTCGEGRVTCLFEDVVPMNYMVYYNFF
AFVLLPLLLMLAIYLRIFLAARRQLKQMESQPLPGERTRSTLQKEVHAAKSLAIIVGLFA
LCWLPLHIINCFTFFCSTCRHAPPWLMYLAIILSHSNSVVNPFIYAYRIREFRQTFRKII
RTHVLRRQEPFQAGGSSAWALAAHSTEGEQVSLRLNGHPLGVWANGSATHSGRRPNGYTL
GLGGGGSAQ-----GSPRDVELPTQERQ-EGQEHPGLRGHLVQARVGASSWSSEFAPS
>P46616
MSSSVYITVELVIAVLAILGNVLVCWAVWINSNLQNVTNYFVVSLAAADIAVGVLAIPFA
ITISTGFCAACHGCLFFACFVLVLTQSSIFSLLTITIDRYIAIRIPLRYNGLVTCTRAKG
IIAICWVLSFAIGLTPMLGWNNCSQPKGDKNHSESCDEGQVTCLFEDVVPMNYMVYYNFF
AFVLVPLLLMLGIYLRIFLAARRQLKQMESQPLPGERTRSTLQKEVHPAKSLAIIVGLFA
LCCLPLNIINCFTFFCPECDHAPPWLMYLTIILSHGNSVVNPLIYAYRIREFRQTFRKII
RSHILRRRELFKAGGTSARASAAHSPEGEQVSLRLNGHPPGVWANGSALRPEQRPNGYVL
GLVSGRSAQRSHGDASLSDVELLSHEHKGTCPESPSLEDPPAHGGAGVS---------
and this is the content of the "jpred_msa.seq.concise" file:
jnetpred:H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,
This is the html code:
<applet code="jalview.bin.JalviewLite" width="100%" height="250" archive="jalviewApplet.jar,JmolApplet-12.1.13.jar">
<param name="showQuality" value="false">
<param name="showConsensus" value="false">
<param name="RGB" value="F2F2FF">
<param name="defaultColour" value="Clustal">
<param name="showAnnotation" value="true">
<param name="jnetfile" value="jpred_msa.seq.concise">
<param name="file" value="TMP/4e28253ce1ab5.fasta">
<param name="PDBFile" value="DATA/PDBs/P30543.pdb P30543">
<param name="PDBFile2" value="DATA/PDBs/P46616.pdb P46616">
<param name="embedded" value="true">
</applet>