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HMMSplicer

swMATH ID: 29568
Software Authors: Dimon, M.T.; Sorber, K.; DeRisi, J.L.
Description: HMMSplicer: A Tool for Efficient and Sensitive Discovery of Known and Novel Splice Junctions in RNA-Seq Data. Here we introduce HMMSplicer, an accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. HMMSplicer identifies more splice junctions than currently available algorithms when tested on publicly available A. thaliana, P. falciparum, and H. sapiens datasets without a reduction in specificity. HMMSplicer was found to perform especially well in compact genomes and on genes with low expression levels, alternative splice isoforms, or non-canonical splice junctions. Because HHMSplicer does not rely on pre-built gene models, the products of inexact splicing are also detected. In addition, HMMSplicer provides a score for every predicted junction allowing the user to set a threshold to tune false positive rates depending on the needs of the experiment. HMMSplicer is implemented in Python. Code and documentation are freely available at the link below.
Homepage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2975632/
Related Software: ARACHNE; SpliceTrap; DWE; CLIPZ; mirTools; miRExpress; TargetSpy; miRNAkey; PatMaN; SeqBuster; ProMiR II; MiRonTop; MiPred; miRanalyzer; DIANA-mirExTra; MiRFinder; HPeak; FindPeaks; mrsFAST; SHARCGS; QSRA
Cited in: 1 Publication

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