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 Cited by 3 Authors 1 Aransay, Ana M. 1 Hackenberg, Michael 1 Rodríguez-Ezpeleta, Naiara Cited in 0 Serials Cited in 2 Fields 1 General and overarching topics; collections (00-XX) 1 Biology and other natural sciences (92-XX) Citations by Year