fahash
Tool to test a DNA sequence for the presence of sequence tagged sites
Install
- All systems
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curl cmd.cat/fahash.sh
- Debian
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apt-get install ncbi-epcr - Ubuntu
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apt-get install ncbi-epcr - Kali Linux
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apt-get install ncbi-epcr - Windows (WSL2)
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sudo apt-get updatesudo apt-get install ncbi-epcr - Raspbian
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apt-get install ncbi-epcr - Dockerfile
- dockerfile.run/fahash
ncbi-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 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.