[ensembl-dev] EnsEMBL compara / protein sequence alignments

[srodriguez]

Dear all,

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.

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.

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).

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).

Would you have a script that already performs my goal?

If not, could you please help me reaching my goal?

Thank you very much in advance.

Best regards,

Sabrina.


*******************************************
Sabrina Rodriguez
Bioinformatics
Département de Génétique animale
Unité GABI
Domaine de Vilvert
78532 Jouy en josas

+33 (0) 1 34 65 29 53
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test.pl
Type: text/x-perl
Size: 2576 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20121022/3878c3af/attachment.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test2.pl
Type: text/x-perl
Size: 2337 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20121022/3878c3af/attachment-0001.bin>