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PatMaN

swMATH ID: 29584
Software Authors: Prüfer, K., Stenzel, U., Dannemann, M., Green, R.E., Lachmann, M., Kelso, J
Description: PatMaN: rapid alignment of short sequences to large databases. Summary: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both queries with and without ambiguity codes can be searched. Search time is short for perfect matches, and retrieval time rises exponentially with the number of edits allowed. Availability: The C++ source code for PatMaN is distributed under the GNU General Public License and has been tested on the GNU/Linux operating system. It is available from http://bioinf.eva.mpg.de/patman.
Homepage: https://academic.oup.com/bioinformatics/article/24/13/1530/238234
Related Software: SHRiMP; PASS; BWA; ZOOM; RazerS; Soap; ARACHNE; SpliceTrap; DWE; CLIPZ; mirTools; miRExpress; TargetSpy; miRNAkey; SeqBuster; ProMiR II; MiRonTop; MiPred; miRanalyzer; DIANA-mirExTra
Referenced in: 2 Publications

Referenced in 1 Serial

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