Re: Database searching help request

alex bell (ehjb@musica.mcgill.ca)
Fri, 15 Oct 1999 11:44:17 -0400

If you have short stretches of protein sequences use FASTA and longer
sequences you should also try blastp searches (raise the EXPECT value in an
advanced blastp search). Of course the longer sequences should also be
searched by FASTA. Also try tblastn searches as conservation may be at the
nucleotide level. Homology is more easily recognized in longer sequences.
Both of the above searches rely on sequence identity in short sequencs. Good
luck. Perhaps also some PDB searches of potential secondary structures - I
do not have experience in this and I am sure much longer sequences are
required - the key to realize here is that poorly related primary sequences
can fold into similar structures. I hope that this stimulates some
discussion for you.
----- Original Message -----
From: Suzanne Perry-Riehm <perry@interchange.ubc.ca>
To: Recipients of ABRF List <abrf@aecom.yu.edu>
Sent: Thursday, October 14, 1999 2:59 PM
Subject: Database searching help request

> I have a client who requested that I search specifically databases looking
> for beta- mannosidases. He cited known sequences of beta mannosidases from
> Human, Capra hircus, Bos taurus and Aspergillus. I performed a digestion
> and generated 6-8 peptide
> sequences to which he requested I use in the search. The origin of the
> digested
> protein is Trichoderma reesei EC 3.2.1.25.
>
> Does anybody out there know if this is possible or have suggestions as to
> how to at least attempt a similar search for this client? I've performed a
> general NR database search but I suppose he would like a more specific
> and limited search.
>
> Thanks in advance for any and all suggestions!
> Suzanne Perry-Riehm
>
> Suzanne C. Perry, Research Associate
> NAPS Protein Sequencing and Peptide Mapping Laboratory
> Biotechnology Department, University of British Columbia
> CANADA
> phone:(604)822-9688( direct) or (604)822-9662 (main) Fax:(604)822-0676
> email:perry@interchange.ubc.ca
> Visit our web page at : www.biotech.ubc.ca/naps/napshome.htm
>