<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
	<maintainer type="project">
		<email>sci-biology@gentoo.org</email>
		<name>Gentoo Biology Project</name>
	</maintainer>
	<longdescription>
		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.
	</longdescription>
</pkgmetadata>