HMMSplicer 0.9.5 – Discovery of Splice Junctions in RNA-Seq data

HMMSplicer 0.9.5


HMMSplicer is 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.


DeRisi LabUCSF




  • Linux/Windows / MacOsX
  • Python





PLoS One. 2010 Nov 8;5(11):e13875.
HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data.
Dimon MT, Sorber K, DeRisi JL.


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