24 lines
1.2 KiB
XML
24 lines
1.2 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="project">
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<email>sci-biology@gentoo.org</email>
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<name>Gentoo Biology Project</name>
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</maintainer>
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<longdescription>
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sim4 is a similarity-based tool for aligning an expressed DNA sequence
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(EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects
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end matches when the two input sequences overlap at one end (i.e., the
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start of one sequence overlaps the end of the other).sim4 employs a
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blast-based technique to first determine the basic matching blocks
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representing the "exon cores". In this first stage, it detects all
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possible exact matches of W-mers (i.e., DNA words of size W) between
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the two sequences and extends them to maximal scoring gap-free
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segments. In the second stage, the exon cores are extended into the
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adjacent as-yet-unmatched fragments using greedy alignment algorithms,
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and heuristics are used to favor configurations that conform to the
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splice-site recognition signals (GT-AG, CT-AC). If necessary, the
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process is repeated with less stringent parameters on the unmatched
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fragments.
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</longdescription>
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</pkgmetadata>
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