sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for a gene. sim4 also detects end matches when two input sequences overlap at one end (that is, the start of one sequence overlaps the end of the other).

See also the sibsim4 program, more recently developed and based on sim4. Sibsim4 is a substantial re-write of sim4 and may offer improved speed and functionality.

sim4 initially employs a blast-based technique to determine the basic matching blocks representing the "exon cores". In this first stage, it detects all possible exact matches of W-mers (i.e., DNA words of size W) between the two sequences and extends them to maximal scoring gap-free segments.

In the second stage, the exon cores are extended into the adjacent as-yet-unmatched fragments using greedy alignment algorithms, and heuristics are used to favour configurations that conform to the splice-site recognition signals (GT-AG, CT-AC). If necessary, the process is repeated with less stringent parameters on the unmatched fragments.

The sim4 package is prepared by Debian-Med and can be installed in Bio-Linux by typing

For further information please see the remote documentation links