PSI-Blast

George Armhold armhold at TOPSIDE.RUTGERS.EDU
Fri Apr 16 10:06:16 EST 1999


Francis Ouellette writes:

> What is parsable today, may not be tomorrow!  (I think they are
> giving us all a heads-up)

Yes, I figured this is what they meant.  It worried me a bit that the
next version may not work with my code, and it worried me that perhaps
some strange input might cause the current code to output in a
different format.  Then again it wasn't much work to write my parser,
so putting in a fix shouldn't be too much trouble.

> Everytime you parse a GB flat-file you loose some information,
> structure that was in the original ASN.1 file, which is the format
> that NCBI maintains all of the sequence data that we use on a
> regular basis, and for which the GBFF is simply a report, a human
> readable format that everybody _loves_ to parse! (see the wonderful
> chapter by Ostell and Kans on the 'NCBI data model' in
> "Bioinformatics: a practical guide to the analysis of genes and
> proteins" edited by Baxevanis and Ouellette.

Funny, I often find the "human readble" to be harder to parse than the
machine variety.  But I haven't done any work with ASN.1 yet.  Thanks
for the book pointer. :-)

-- 
George Armhold                    PGP Key: [02D2EBE5]
Rutgers University            Fingerprint: [51 8B A4 B0 7A 71 7C E7]
Bioinformatics Initiative                  [85 DE 13 99 0B 68 5F 92]




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