A Graph Theoretic Algorithm for Removing Redundant Protein Sequences

Many biological sequence databases have redundant sequences which are not helpful to statistical analysis and require more computational time and resources to process. This lead us to design a new and fast program to generate a non-redundant sequence set. A graph theoretic algorithm was designed to process BLAST output and remove redundant proteins from a protein sequence database. We have developed a program named BlastCuller which can be used to generate a non-redundant protein database. BlastCuller is a flexible program with a parameter of sequence similarity cutoff, which can be a decimal from 0.0 to 1.0. This program can be downloaded from http://pcal.biosino.org/BlastCuller.html.