Package: ncbi-epcr (2.3.12-1)

[ Source: epcr  ]

Tool to test a DNA sequence for the presence of sequence tagged sites

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 discontigous 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.

Tags: Field: Biology, Bioinformatics, Implemented in: C++, User Interface: Command Line, Role: Program, Scope: Utility, Purpose: Checking, Searching, Supports Format: Plain Text

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Architecture	Package Size	Installed Size	Files
amd64	194.5 kB	520.0 kB	[list of files]
armel	183.7 kB	472.0 kB	[list of files]
i386	187.9 kB	476.0 kB	[list of files]
ia64	268.8 kB	892.0 kB	[list of files]
kfreebsd-amd64	194.6 kB	462.0 kB	[list of files]
kfreebsd-i386	187.7 kB	426.0 kB	[list of files]
mips	200.9 kB	668.0 kB	[list of files]
mipsel	200.9 kB	668.0 kB	[list of files]
powerpc	201.6 kB	544.0 kB	[list of files]
s390	191.6 kB	504.0 kB	[list of files]
sparc	196.8 kB	528.0 kB	[list of files]