Comparison of biological sequence to one another is commonly used to determine similarity and relationships between sequences. Tools like BLAST are frequently used to compare sequences, however, with the availibility of large volumes of genomic sequence data, such large-scalre comparisons are computationally intensive. Large-scale protein sequence comparisons at chromosome/genome level are a common practise especially in comparative genomics (gene matching) and ortholog identification etc. We have developed Afree, a rapid large-scale protein sequecne comparison tool that can perform all-against-all sequence comparison as a single bulk task and is faster than commonly used tools such as BLAST. Afree performs sequence comparison between bacterial genomes in a matter of seconds.

Input a pair of proteome files containing fasta formatted protein sequnces, and the result shows all sequence pairs that share a user prescribed similarity threshold.

Afree is an alternative to BLASTp for the purpose of all-against-all sequence comparison. Further, afree output can be readily used as input in other tools for gene matching, orthologs identification, synteny analysis, phylogenetic analysis and gene annotation.

The Afree tool is a easy to use standalone application that takes as input two FASTA formated proteome files and generates table of pairwise similarities.

Download - 29 Nov 2011


Binaries are free for non-commercial use.