[ensembl-dev] EnsEMBL compara / protein sequence alignments

[Javier Herrero]

Dear Sabrina

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.

Your strategy using the ENSEMBLGENE was correct. Indeed, you get two 
proteins aligned. I believe this is what you want, isn't it?

I have added a few comments. Let me know if there something that is not 
clear.

Javier

On 22/10/12 15:58, srodriguez wrote:
> 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
>
>
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-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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