Tag: Discovery

nFuse 0.2.1 – Discovery of Complex Genomic Rearrangements in Cancer

nFuse 0.2.1

:: DESCRIPTION

nFuse is a tool for detecting fusion transcripts and associated complex genomic rearrangements from matched RNA-seq and whole genome shotgun sequencing.nFuse predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).

::DEVELOPER

Andrew McPherson (andrew.mcpherson@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 nFuse

:: MORE INFORMATION

Citation:

McPherson AW, Wu C, Wyatt A, Shah SP, Collins C, Sahinalp SC.
nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing.
Genome Res. 2012 Jun 28.

Sniper 1.6.4 – SNP Discovery Utilizing Multi-mapping Reads

Sniper 1.6.4

:: DESCRIPTION

Sniper is a Bayesian probabilistic model that enables SNP discovery in both unique and repetitive regions of a genome by utilizing the information from multiply-mapped sequence reads.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux/ MacOsX/ Windows
  • Python

:: DOWNLOAD

 Sniper

:: MORE INFORMATION

Citation

Genome Biol. 2011 Jun 20;12(6):R55. doi: 10.1186/gb-2011-12-6-r55.
Sniper: improved SNP discovery by multiply mapping deep sequenced reads.
Simola DF, Kim J.

CPD r136 – Correlated Pattern Discovery program

CPD r136

:: DESCRIPTION

CPD is a program that solves the generalized color set size problem in linear time.

::DEVELOPER

Hideo Bannai 

:: REQUIREMENTS

  • Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

  CPD

:: MORE INFORMATION

Citation

Hideo Bannai, Heikki Hyyrö , Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, and Satoru Miyano,
“Finding Optimal Pairs of Patterns“,
In Proceedings of the 4th International Workshop on Algorithms in Bioinformatics (WABI 2004), LNBI 3240:450-462, (2004).

RBPSpot – Learning on Appropriate Contextual Information for RBP Binding Sites Discovery

RBPSpot

:: DESCRIPTION

BPSpot is a tool to identify RBP binding spots in RNA.

::DEVELOPER

SCBB-LAB (Studio of Computational Biology and Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

RBPSpot

:: MORE INFORMATION

Citation

Sharma NK, Gupta S, Kumar A, Kumar P, Pradhan UK, Shankar R.
RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery.
iScience. 2021 Oct 30;24(12):103381. doi: 10.1016/j.isci.2021.103381. PMID: 34841226; PMCID: PMC8605353.

Freddie v0.3.1 – Long Reads Isoform Discovery Tool

Freddie v0.3.1

:: DESCRIPTION

Freddie: Annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • conda
  • Python

:: DOWNLOAD

Freddie

:: MORE INFORMATION

Citation

Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms
Baraa Orabi, Brian McConeghy, Cedric Chauve, Faraz Hach
bioRxiv 2021.01.20.427493; doi: https://doi.org/10.1101/2021.01.20.427493

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.

 

Cake 1.0 – Somatic Mutation Discovery

Cake 1.0

:: DESCRIPTION

Cake is a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.

::DEVELOPER

Adams Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl

:: DOWNLOAD

 Cake

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2208-10. doi: 10.1093/bioinformatics/btt371. Epub 2013 Jun 25.
Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes.
Rashid M1, Robles-Espinoza CD, Rust AG, Adams DJ.

Vacceed 1.1 – in silico Vaccine Discovery pipeline for Eukaryotic Pathogens

Vacceed 1.1

:: DESCRIPTION

Vacceed is a highly configurable and scalable framework designed to automate the process of high-throughput in silico vaccine candidate discovery for eukaryotic pathogens.

::DEVELOPER

Vacceed team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Vacceed

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 29. pii: btu300. [Epub ahead of print]
Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology.
Goodswen SJ, Kennedy PJ, Ellis JT.

CisModule 20051205 – De novo Discovery of Cis-regulatory Modules

CisModule 20051205

:: DESCRIPTION

CisModule: A Bayesian module sampler by hierachical mixture modeling

::DEVELOPER

Qing Zhou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 CisModule

:: MORE INFORMATION

Citation

Zhou, Q. and Wong, W.H. (2004).
CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling.
Proceedings of the National Academy of Sciences USA, 101: 12114-12119.

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.

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