Ensembl Mysql Peptide Sequence

Question

[Barby]

Hi all, I'm playing with the mysql server for ENSEMBL

I am trying get the peptide sequence from homo sapiens. I can see he tables, but how i can get all peptide sequence from it?

thanks

B

Answer 1

[Bert Overduin]

Hello,

Peptide sequences are not stored in the Ensembl core database, but calculated on the fly from the information present in the transcript and translation tables. As mentioned above, you can retrieve files containing genome-wide peptide sets from our ftp site. If you are interested in subsets of peptide sequences, you may want to retrieve these using either BioMart or the Perl API.

Hope this helps.

Answer 2

[Ahdf-Lell-Kocks]

You can also get them in fasta format from the compara MySQL database like so:

mysql -h ensembldb.ensembl.org -uanonymous -P5306 ensembl_compara_65 -N -e "\
select concat_ws('#', concat('>',m.stable_id), s.sequence) from sequence s, \
member m where m.source_name='ENSEMBLPEP' and m.sequence_id=s.sequence_id and \
m.genome_db_id=(select genome_db_id from genome_db where name='homo_sapiens')" |\
perl -pe 's/\#/\n/' > homo_sapiens.pep

It may take a while to run the query...

Answer 3

[brentp]

I am not sure you can get peptide sequence via the MySQL API, but you can download a FASTA file here.

I got there from this page and the filtered to 'Homo sapiens'