PFMFind: a system for discovery of peptide homology and function

Details PFMFind: a system for discovery of peptide homology and function PFMFind: a system for discovery of peptide homology and function

2006-03-09

arxiv.org/abs/q-bio/0603011v1

Biology

Quantitative Biology

Other Quantitative Biology

4 pages, 1 figure

Scientific paper

Protein Fragment Motif Finder (PFMFind) is a system that enables efficient discovery of relationships between short fragments of protein sequences using similarity search. It supports queries based on score matrices and PSSMs obtained through an iterative procedure similar to PSI-BLAST. PSSM construction is customisable through plugins written in Python. PFMFind consists of a GUI client, an algorithm using an index for fast similarity search and a relational database for storing search results and sequence annotations. It is written mostly in Python. All components communicate between themselves using TCP/IP sockets and can be located on different physical machines. PFMFind is available for UNIX and Windows platforms.

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