ncbi-epcr
Tool to test a DNA sequence for the presence of sequence tagged sites
Command lineScience
Not tested on a device yet. What that means
Commands in the package
e-PCRfahashfamapre-PCR
About ncbi-epcr
From Debian's package description
Electronic PCR (e-PCR) is computational procedure that is used to identify sequence tagged sites(STSs), within DNA sequences. e-PCR looks for potential STSs in DNA sequences by searching for subsequences that closely match the PCR primers and have the correct order, orientation, and spacing that could represent the PCR primers used to generate known STSs.
The new version of e-PCR implements a fuzzy matching strategy. To reduce likelihood that a true STS will be missed due to mismatches, multiple discontiguous words may be used instead of a single exact word. Each of this word has groups of significant positions separated by 'wildcard' positions that are not required to match. In addition, it is also possible to allow gaps in the primer alignments.
The main motivation for implementing reverse searching (called Reverse e-PCR) was to make it feasible to search the human genome sequence and other large genomes. The new version of e-PCR provides a search mode using a query sequence against a sequence database.
This program is retired upstream and it is suggested to use Primer-Blast https://www.ncbi.nlm.nih.gov/tools/primer-blast/ instead.
From Debian's description of the ncbi-epcr package, under that package's license.
Dependencies
Depends on
libc6libgcc-s1libstdc++6
Related apps
- entpseudorandom number sequence test programCommand line
- wisecomparison of biopolymers, like DNA and protein sequencesCommand line
- prankProbabilistic Alignment Kit for DNA, codon and amino-acid sequencesCommand line
- staden-io-lib-utilsprograms for manipulating DNA sequencing filesCommand line
- mapdamagetracking and quantifying damage patterns in ancient DNA sequencesCommand line
- mipeTools to store PCR-derived dataCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the ncbi-epcr package, under that package's license.
- Description: Debian's description of the ncbi-epcr 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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