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Dear Sabrina<br>
<br>
I have modified the script slightly only. Essentially, I have
removed some bits that were not required and cleaned up the code a
little. I have also added the possibility of specifying the query
and the target species in the command line. Last, I have also
changed the script to output the alignments into separate files.<br>
<br>
Your strategy using the ENSEMBLGENE was correct. Indeed, you get two
proteins aligned. I believe this is what you want, isn't it?<br>
<br>
I have added a few comments. Let me know if there something that is
not clear.<br>
<br>
Javier<br>
<br>
<div class="moz-cite-prefix">On 22/10/12 15:58, srodriguez wrote:<br>
</div>
<blockquote
cite="mid:20121022165801.12520rfldsin1kw0@www2.jouy.inra.fr"
type="cite">Dear all,
<br>
<br>
I would like to use compara EnsEMBL API to get the aligned protein
sequences of a query animal with homologous protein sequences from
other species.
<br>
<br>
The script would take as input the query specie name, (and if
possible the hit species names). The script would get the proteins
of the query organism, then the homologous protein sequences, and
then retrieves 1 file per protein query sequence containing the
alignment of the query (placed as the first sequence) and then the
other specie protein sequences aligned.
<br>
<br>
I was thinking about using an "homology adaptor" with ENSEMBLPEP,
so I started a script that way, but I do not obtain any results
with ENSEMBLPEP and the results with ENSEMBLGENE are 2 sequences
per alignment (see script attached).
<br>
<br>
I also tried with "families", but sometimes, I do not get the
protein sequence for my specie query in the sequence alignment
even though I searched by using my taxon id (script N#2 attached).
<br>
<br>
Would you have a script that already performs my goal?
<br>
<br>
If not, could you please help me reaching my goal?
<br>
<br>
Thank you very much in advance.
<br>
<br>
Best regards,
<br>
<br>
Sabrina.
<br>
<br>
<br>
*******************************************
<br>
Sabrina Rodriguez
<br>
Bioinformatics
<br>
Département de Génétique animale
<br>
Unité GABI
<br>
Domaine de Vilvert
<br>
78532 Jouy en josas
<br>
<br>
+33 (0) 1 34 65 29 53<br>
<br>
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<br>
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
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