sim4
tool for aligning cDNA and genomic DNA
Command lineScience
Not tested on a device yet. What that means
Commands in the package
sim4
About sim4
From Debian's package description
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.
From Debian's description of the sim4 package, under that package's license.
Dependencies
Depends on
libc6
Related apps
- sim4dbbatch spliced alignment of cDNA sequences to a target genomeCommand line
- pal2nalconverts proteins to genomic DNA alignmentCommand line
- spalnsplicing-aware transcript-alignment to genomic DNACommand line
- ssakegenomics application for assembling millions of very short DNA sequencesCommand line
- lastzpairwise aligning DNA sequencesCommand line
- bedtoolssuite of utilities for comparing genomic featuresCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the sim4 package, under that package's license.
- Description: Debian's description of the sim4 package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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