reformatting gb/sp/pir retrievals

Harry Mangalam mangalam at uci.edu
Fri May 6 15:13:08 EST 1994


> Dear netters.
> 
>         I am looking for a way to reformat the documents I retrieve from genebank, swiss-protein or other databanks to either format accepted by ClustalV for example. The interfaces I have are Unix and Mac.
> 
> I have been using readseq but with unsatisfactory results. are there any alternatives? Are there any programms, that could split multiple sequence retrievals into multiple single-sequence files?
> 
> thanx for any help.
> 
> Helge
Try readseq by Don Gilbert (another national treasure) available free from
his treasure trove of molbio delights at ftp.bio.indiana.edu (gopher or
ftp).  Versions available for everything that has a C compiler. 
(Inter)converts the following formats:

         1. IG/Stanford           10. Olsen (in-only)
         2. GenBank/GB            11. Phylip3.2
         3. NBRF                  12. Phylip
         4. EMBL                  13. Plain/Raw
         5. GCG                   14. PIR/CODATA
         6. DNAStrider            15. MSF
         7. Fitch                 16. ASN.1
         8. Pearson/Fasta         17. PAUP/NEXUS
         9. Zuker (in-only)       18. Pretty (out-only)
-- 

Harry Mangalam, VCO/Micro+Mol Genetics, Irvine Hall, College of Medicine, 
UC Irvine, Irvine, CA, 92717, Vox:(714) 856-4824, Fax:(714) 725-2118,
mangalam at uci.edu

There's no better glory, when it all gets harried, to be laughing in the
midst of it all.   --- Doug and the Slugs ---




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