PFMFind: a system for discovery of peptide homology and function.
Protein Fragment Motif Finder (PFMFind) is a system that enables e cient discovery of relationships between short fragments of protein sequences using similarity search. It supports queries based on amino acid similarity matrices and position specific score matrices (PSSMs) obtained through an iterative procedure. PSSM construction is customisable through plugins written in Python. PFMFind consists of a GUI client, an index for fast similarity search and a relational database for storing search results and sequence annotations. It is written mostly in Python. The components of PFMFind communicate through TCP/IP sockets and can be located on different physical machines. PFMFind is freely available for download (under a GPL licence) from http://pfmfind.stojmirovic.org.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States.
Aleksandar
A
Stojmirović
School of Engineering and Computer Science, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand.
Peter
P
Andreae
Riddet Institute, Massey University, PB 11 222, Palmerston North 4442, New Zealand.
Mike
M
Boland
School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand.
Thomas William
TW
Jordan
Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Ave., Ottawa, ON K1N 6N5, Canada.
Vladimir G
VG
Pestov
indexing; protein fragments; similarity search