Tag: Splice Junction

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

HMMSplicer 0.9.5

:: DESCRIPTION

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.

::DEVELOPER

DeRisi Lab, UCSF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows / MacOsX
  • Python

:: DOWNLOAD

 HMMSplicer

:: MORE INFORMATION

Citation

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.

 

MapSplice 2.1.8 – Mapping of RNA-seq reads for Splice Junction Discovery

MapSplice 2.1.8

:: DESCRIPTION

MapSplice is an algorithm for mapping RNA-seq data to reference genome for splice junction discovery.  MapSplice algorithm to detect splice junctions without any dependence on splice site features. This enables MapSplice to discover non-canonical junctions and other novel splicing events, in additional to the more common canonical junctions.

::DEVELOPER

Bioinformatics Lab @CS.UKy.edu

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 MapSplice

:: MORE INFORMATION

Citation

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery.
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J.
Nucleic Acids Res, 38(18):e178, 2010.

SpliceMap 3.3.7 – Splice Junction Discovery Using RNA-Seq

SpliceMap 3.3.7

:: DESCRIPTION

SpliceMap is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths.

::DEVELOPER

the Wong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SpliceMap

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Aug;38(14):4570-8. Epub 2010 Apr 5.
Detection of splice junctions from paired-end RNA-seq data by SpliceMap.
Au KF, Jiang H, Lin L, Xing Y, Wong WH.

TrueSight 0.06 – Self-training Algorithm for Splice Junction Detection using RNA-seq

TrueSight 0.06

:: DESCRIPTION

TrueSight is a self-training algorithm for splice junction detection using RNA-seq

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TrueSight

:: MORE INFORMATION

Citation

Li Y, Li H, Burns P, Borodovsky M, Robinson GE, and Ma J.
TrueSight: self-training algorithm for splice junction detection using RNA-seq.
To appear in Proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2012.