[EMBOSS] Working with Geneseq databases

[Wells, Isabelle]

Hi Daniel,
We index the geneseq databases in the EMBL format. The problem with Geneseq format is that each entry has several lines starting with "SQ   ". Therefore in order to make this work you just need to write a program which only prints the first line starting with "SQ   " in each entry and skips the following SQ lines.
Hope this helps!

Best regards,
Isabelle Wells
F. Hoffmann-La Roche Ltd 


-----Original Message-----
From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Rozenbaum, Daniel (Biocceleration Inc)
Sent: Wednesday, 6. February 2013 16:50
To: emboss at lists.open-bio.org
Subject: [EMBOSS] Working with Geneseq databases

Dear all,

Does anyone have experience getting EMBOSS to work with the Geneseq database distributed by Thomson Reuters ( http://thomsonreuters.com/products_services/science/science_products/a-z/geneseq/ ) ? This database comes in "EMBL-like" format that uses some line codes that are not defined in EMBL format proper, which in our experiments has caused problems when, for example, trying to index these databases as EMBL-formatted.
--
Daniel Rozenbaum
Biocceleration, Inc.
OCIO/Office of Application Engineering and Development/Patent System Division
600 Dulany St., Alexandria, VA 22314
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