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Diffstat (limited to 'sci-biology/sim4/metadata.xml')
| -rw-r--r-- | sci-biology/sim4/metadata.xml | 21 |
1 files changed, 21 insertions, 0 deletions
diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml new file mode 100644 index 000000000000..ea9731279003 --- /dev/null +++ b/sci-biology/sim4/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <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> |