Hi, How about using fastacmd. If you have your genome sequence formatted with formatdb (in blast algorithm), you can easily use fastacmd to retrieve any sequence you want :
fastacmd -d (your formatted genome db) -s (sequence name) (location) On Wed, Feb 4, 2009 at 3:32 AM, Rodrigo Lopez <[email protected]> wrote: > Hi Nermin, > > To complement Guy's reply: You could also use the EMBLCDS database. This > one contains all CDSs in EMBL-Bank (soon to be called ENA = European > Nucleotide Archive). This one is available via the EBI's ftp server at > pub/databases/embl/cds. The identifiers in this database correspond to the > protein_id feature in the EMBL-Bank Feature Table which maps each CDS to > corresponding protein translation. These in turn can be identified in > UniProtKB. Please see the README.txt file at: > > ftp.ebi.ac.uk/pub/databases/embl/cds/README.txt > > for further details. > > Further to the above, and depending on the proteome in question, you could > have a look at the integr8 directory on the ftp server as well: > > ftp.ebi.ac.uk/pub/databases/integr8 > > In here you will find the proteomes of more than 1600 organisms, mainly > bacteria and archea, but also human, rat, mouse, etc. > > R:) > > > > Nermin Celik wrote: > >> Hi, >> >> I have the CDS section of a feature table and a genome of an organism. >> Which EMBOSS program will allow me to extract the coding regions defined >> in the CDS file from the genome and then translate them to protein >> sequences? >> >> Example of CDS file: >> FT CDS 166..231 >> FT /systematic_id="ROD00001" >> FT CDS 313..2775 >> FT /systematic_id="ROD00011" >> FT CDS 2778..3707 >> >> Thank you. >> Nermin >> >> _______________________________________________ >> EMBOSS mailing list >> [email protected] >> http://lists.open-bio.org/mailman/listinfo/emboss >> > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss > -- -------------------------------------------------------- Magdy S. Alabady, PhD Energy Bioscience Institute (EBI) Institute for Genome Biology (IGB) University of Illinois At Urbana-Champaign, Illinois ------------------------------------------------------ Imagination is more important than knowledge. For knowledge is limited, whereas imagination embraces the entire world, stimulating progress, giving birth to evolution.. .....Albert Einstein ------------------------------------------------------------- _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
