Tag: RNA-seq data

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.

 

PASSion 1.2.1 – Pattern Growth algorithm based Pileline for Splice Site Detection in Paired-end RNA-Seq data

PASSion 1.2.1

:: DESCRIPTION

PASSion uses the mapped read in a pair as anchor and then uses a high resolution algorithm, pattern growth, to remap the proximal and distal fragments of the unmapped read to a local region of the reference indicated by the mate. It is capable of identifying both known and novel canonical and non-canonical junctions with SNP or sequencing error tolerance.

::DEVELOPER

Yanju Zhang (Leiden University Medical Center, The Netherlands): y.zhang AT lumc.nl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PASSion

:: MORE INFORMATION

Citation:

PASSion: A Pattern Growth Algorithm Based Pipeline for Splice Junction Detection in Paired-end RNA-Seq Data
Yanju Zhang; Eric-Wubbo Lameijer; Peter A.C. ‘t Hoen; Zemin Ning; P. Eline Slagboom; Kai Ye
Bioinformatics 2012; doi: 10.1093/bioinformatics/btr712

SpliceGrapher 0.2.7 – Creat Splice Graphs from RNA-Seq data

SpliceGrapher 0.2.7

:: DESCRIPTION

SpliceGrapher is a tool for predicting splice graphs and alternative splicing patterns using next generation sequencing data, guided by gene models and EST data.

::DEVELOPER

Asa Ben-Hur

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SpliceGrapher

:: MORE INFORMATION

Citation

Genome Biol. 2012 Jan 31;13(1):R4. [Epub ahead of print]
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.
Rogers MF, Thomas J, Reddy AS, Ben-Hur A.

SnowShoes-FTD – Find Fusions from RNA-Seq data

SnowShoes-FTD

:: DESCRIPTION

SnowShoes-FTD is a bioinformatics tool to identify fusion transcripts from paired-end transcriptome sequencing data. The tool employs multiple steps of false positive filtering and nominates the fusion candidates with high confidence (approaching 100% true positive rate). The unique features of SnowShoes-FTD include: (i) the ability to discover multiple fusion isoforms in which the two gene partners give rise to transcripts with different junctions; (ii) prediction of potential fusion mechanisms including inversion, translocation, and/or interstitial deletions; (iii) identification of whether the junction point in a fusion transcript occurs at the boundaries of known exons which implies the fusion events might have happened inside an intron in DNA and transcribed to the fusion transcript.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Please contact the author, Yan W. Asmann, Ph.D. smann.yan@mayo.edu

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2011 Aug;39(15):e100. Epub 2011 May 27.
A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.
Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA.

TeXP v1.0 – Quantifying Abundances of Transposable Elements transcripts from RNA-Seq data

TeXP v1.0

:: DESCRIPTION

TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TeXP

:: MORE INFORMATION

Citation:

PLoS Comput Biol. 2019 Aug 19;15(8):e1007293. doi: 10.1371/journal.pcbi.1007293. eCollection 2019 Aug.
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.
Navarro FC, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB

TSSpredator 1.07.1beta – Comparative TSS prediction from RNA-seq data

TSSpredator 1.07.1beta

:: DESCRIPTION

TSSpredator is a Java program for the automated detection and classification of TSS from RNA-seq data.TSSpredator reads RNA-seq data in the form of simple wiggle files and performs a genome wide comparative prediction of TSS, for example between different growth conditions.

::DEVELOPER

Research Group “Integrative Transcriptomics” , Center for Bioinformatics Tübingen, University of Tübingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOS
  • Java

:: DOWNLOAD

TSSpredator

:: MORE INFORMATION

Citation

Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R, Nieselt K, Sharma CM.
High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates.
PLoS Genet. 2013 May ; 9(5): e1003495