  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.
