Tool for aligning cDNA and genomic DNA

Some information about sim4 from the Debian Med project.

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

 sim4 employs a blast-based technique to first 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 favor
 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.


Homepage: http://www.bx.psu.edu/miller_lab/

Please read the man page of this project:

     man sim4
