Software to Parse Feature Table

Reinhard Doelz doelz at comp.bioz.unibas.ch
Tue Sep 21 23:53:44 EST 1993


In article <16C50DE8D.A428ENDE at HASARA11.SARA.NL>, A428ENDE at HASARA11.SARA.NL writes:
|> In article <CDEz1A.7s3 at usenet.ucs.indiana.edu>
|> wfischer at bio.indiana.edu (Will Fischer) writes:
|>  
|> >I need to extract given pieces of sequence from a set of EMBL/GenBank
|> >flat file entries (as retrieved from NCBI's email server), using ranges
|> >defined in the features table.  For example, I'd like to be able to
|> >extract, from a set of entries, the DNA sequence for each exon, or
|> >again for every complete CDS feature (all exons assembled).
|> >

> A few months ago I wanted all the CDS from Chlamydomonas sequences. Because I d
|> idn'T konow of any software I wrote a TurboPascal routine to do it. However the
|> re are a lot of strange ways in the feature table to give the CDS (I found at l
|> east five different ways!). Therefor the program isn't straight forward and is
|> sometimes not very elegant. I think you can understand how it is working, so I
|> can mail it if you want. It is a unit for TurboPascal 5.0 or greater and works
|> on a DOS machine.

The SRS program from Thure Etzold runs on VMS and a zoo of UNIXes ; it does what you want after GCG reformatting. 

Regards
Reinhard


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