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Protein Search

gdavis at uoknor.edu gdavis at uoknor.edu
Thu Jun 27 16:17:15 EST 1996

Dear colleagues,

Does anyone know of a computer program that will search Swiss Protein
Databank files using criteria that is based on a user defined
mathematical expression using amino acid sequence data?

In other words, I must count the numbers of particular amino acids
using a Swiss Protein Databank file , plug them into a mathematical
expression,  and then see if the output is within the range I want.
The key point is that I want to be able to do this for hundreds (or
thousands if possible) of proteins at a time.  So, the program must be
able to access a large directory (maybe even Swiss-Prot itself)
containing these files.

In the event that there is no pre-existing program, I am attempting to
write a program in C that will do this.  If anyone is proficient in
writing C programs that do multiple file input (or even just basic
text searching), I would love to ask you some questions about the best
way to go about this.  I have a program that will work for one file at
a time, but I would much prefer to automate it.

Greg Davis
gdavis at uoknor.edu
University of Oklahoma
School of Chemical Engineering and Materials Science
Biotechnology Research

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