BioPerl- blastcl3-parse the BLAST

[ZBa...@gmail.com]

Dear Seemann

I am new to Perl, and my background is Biology. I was wondering if you
could be of help with the follwoing problem.


1) I have downloaded NetBlast
2) I have Installed BioPerl
3) I have 36 fasta formate files (e.g. 1B94.fasta.txt, 1DNK.fasta.txt
and so on)
4) I want to write a Perl script that uses the blastcl3 program
(NetBlast) to perform BLAST queries on the 36 DNA-binding proteins
using the Bio::SearchIO module to parse the BLAST result and print the
following information and from the first BLAST hit from each query to
a file:
Protein name (or just the file name of the protein)
Hit name
Percent identity
HSP length
HSP start
HSP end
Number of identical residues
Number of gaps

5) Write a DBI script that creates a table called blast_hits in a
database named DNA-bp. The table should have a field for each of the 8
parameters above (plus one for the ID). This script should create the
table, load the data from the output file of the previous script,
query the newly populated database for all information for each DNA-
bp

[Edward Salinas]

Learn about DBI here....(I got these links from googling "perl dbi tutorial")

http://www.perl.com/pub/a/1999/10/DBI.html
http://www.sol4.net/projects/project4.shtml

Assuming you have #4 complete this will help you with #5.
It looks like you should learn some database basics and some SQL too.

It could take a long time to write step-by-step instructions, but the
above link and tidbits of information should point you in the right
direction/path and at least give you some ideas.