Tag: Rapid Alignment

ProbeMatch – Rapid Alignment of Oligonucleotides to Genome

ProbeMatch

:: DESCRIPTION

ProbeMatch is a sequence alignment program designed for matching a large set of oligonucleotide sequences against a genome database using gapped alignments. Unlike existing tools such as ELAND and MAQ which only perform ungapped alignments allowing at most 2-3 mismatches, ProbeMatch generates both ungapped and gapped alignments allowing up to 3 errors including insertion, deletion, and mismatch.

::DEVELOPER

Jignesh M. Patel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 ProbeMatch

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Jun 1;25(11):1424-5. doi: 10.1093/bioinformatics/btp178. Epub 2009 Apr 7.
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.
Kim YJ1, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM.

MicroRazerS 1.0 – Rapid Alignment of small RNA reads

MicroRazerS 1.0

:: DESCRIPTION

MicroRazerS is a tool optimized for mapping small RNAs onto a reference genome. It is an order of magnitude faster than Mega BLAST and comparable in speed with other short read mapping tools. In addition, it is more sensitive and easy to handle and adjust.

::DEVELOPER

Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert and Silke Sperling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MicroRazerS

:: MORE INFORMATION

Citation

Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert and Silke Sperling.
MicroRazerS: rapid alignment of small RNA reads.
Bioinformatics (2010) 26 (1): 123-124