Database file format conversion

Humberto Oritz-Zuazaga zuazaga at ucunix.san.uc.edu
Mon Sep 30 10:10:30 EST 1991

In article <1991Sep30.132401.4021 at murdoch.acc.Virginia.EDU> wrp at biochsn.acc.Virginia.EDU (William R. Pearson) writes:
>In article <9109301300.AA05395 at lux.think.com> jones at Think.COM (Robert Jones) writes:
>>I was thinking about setting up an equivalent for sequence files and
>>database extraction could readily fall into this. For someone familiar
>>with UNIX it would be straightforward to use and some simple wrapper
>	I am not so enthusiatic about a portable filter approach for
>two reasons
>	1) The number one concern in searching databases is speed.
>Portable filters might easily double the amount of time required to
>search a database.

I think you misunderstood, you don't translate the database into your
format, you translate your search sequence into the databases format. 
Unless your search seq. is huge I don't see it affecting search times

>Alternately, it may not be possible to implement
>them, since FASTA and BLAST need to go back into the database a second
>time to reread a subset of sequences.  Random access is required.

What's to prevent random access?

>What is needed is a
>simple, efficient to implement, interface to library reading routines.
>One of the shortcomings of BLAST is that it only reads its own format

Again, I think you misunderstand. Genbank has a BLAST server, you've got
a sequence, translate your sequence and send your query in.
Humberto Ortiz-Zuazaga                      INTERNET: zuazaga at ucunix.san.uc.edu
Dept. of Physiology & Biophysics              BITNET:              picone at ucbeh
University of Cincinnati                         CIS:                72301,2303

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