sim4db
batch spliced alignment of cDNA sequences to a target genome
Command lineScience
Not tested on a device yet. What that means
Commands in the package
sim4dbcleanPolishescomparePolishesconvertPolishesconvertToAtacconvertToExtentdepthOfPolishesdetectChimerafilterPolishesfixPolishesIIDheadPolishesmappedCoveragemergePolishesparseSNPpickBestPolishpickUniquePolishplotCoverageVsIdentityrealignPolishesremoveDuplicatereportAlignmentDifferencessortPolishessummarizePolishesuniqPolishesvennPolishes
About sim4db
From Debian's package description
Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc algorithms to determine the alignments, but incorporates a fast sequence indexing and retrieval mechanism, implemented in the sister package 'leaff', to speedily process large volumes of sequences.
While sim4db produces alignments in the same way as sim4 or sim4cc, it has additional features to make it more amenable for use with whole-genome annotation pipelines. A script file can be used to group pairings between cDNAs and their corresponding genomic regions, to be aligned as one run and using the same set of parameters. Sim4db also optionally reports more than one alignment for the same cDNA within a genomic region, as long as they meet user-defined criteria such as minimum length, percentage sequence identity or coverage. This feature is instrumental in finding all alignments of a gene family at one locus. Lastly, the output is presented either as custom sim4db alignments or as GFF3 gene features.
This package is part of the Kmer suite.
From Debian's description of the sim4db package, under that package's license.
Dependencies
Depends on
libc6libgcc-s1libstdc++6
Recommends
leaffkmer-examples
Related apps
- atacgenome assembly-to-assembly comparisonCommand line
- leaffbiological sequence library utilities and applicationsCommand line
- merylin- and out-of-core kmer counting and utilitiesCommand line
- fsaFast Statistical Alignment of protein, RNA or DNA sequencesCommand line
- gbrowseGMOD Generic Genome BrowserCommand line
- samtoolsprocessing sequence alignments in SAM, BAM and CRAM formatsCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the sim4db package, under that package's license.
- Description: Debian's description of the sim4db package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.