Difference between revisions of "HMMSplicer"

Jump to navigation Jump to search
m (Text replacement - "#uppercase" to "uc")
Line 33: Line 33:
==System Variables==
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR
* HPC_{{uc:{{#var:app}}}}_DIR
{{#if: {{#var: conf}}|==Configuration==
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 21:21, 6 December 2019


hmmsplicer website  

HMMSplicer, is an implementation of 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.

Required Modules


  • hmmsplicer - installation directory

System Variables



  • Validated 4/5/2018