The following module was proposed for inclusion in the Module List:
modid: Bio::RNA::SpliceSites::Scoring::MaxEntScan
DSLIP: bdpf2
description: Pre-mRNA splice site scoring by max entropy
userid: BRYKETOS (Brian Sebastian Cole)
chapterid: 23 (Miscellaneous_Modules)
communities:
https://github.com/bryketos/Bio-RNA-SpliceSites-Scoring-MaxEntScan
similar:
rationale:
Modern genomics pipelines to assess pre-mRNA splicing in dynamic
contexts such as alternative splicing need modular splice site
strength quantification tools. In 2004, Gene Yeo and Chris Burge at
MIT released a Perl tarball for scoring of pre-mRNA splice sites by
a maximum entropy-based approach, which they called maxEntScan. Fast
forward 10 years and integrated Perl pipelines are commonplace in
genomic data analysis, yet the only existing way to integrate the
maxEntScan programs into a pipeline is through system calls, with no
documentation or testing provided in the original maxEntScan
programs. To address this, I refactored the algorithm of Yeo and
Burge into a Perl module that can export splice site scoring
functions into other namespaces. Additionally, I add version
control, testing, documentation, and an adaptable package-based
splice model for the creation of novel maximum entropy-based splice
models as detailed in the original maxEntScan program from 2004. Of
note: I contacted the original author Dr. Gene Yeo, currently a
professor at UCSD, and he consented to the development of this
current distribution and its upload to PAUSE. My thesis advisor also
consented. Cheers!
enteredby: BRYKETOS (Brian Sebastian Cole)
enteredon: Sun Aug 17 20:38:33 2014 UTC
The resulting entry would be:
Bio::RNA::SpliceSites::Scoring::
::MaxEntScan bdpf2 Pre-mRNA splice site scoring by max entropy BRYKETOS
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