discoSnp 2.5.4 – Discovering SNPs without requiring any reference Genome

discoSnp 2.5.4

:: DESCRIPTION

Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).

::DEVELOPER

Genome Analysis Toolbox with de-Bruijn graph (GATB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

discoSnp

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2014 Mar;14(2):393-400. doi: 10.1111/1755-0998.12179. Epub 2013 Nov 11.
Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms.
Quillery E1, Quenez O, Peterlongo P, Plantard O.

MITE-Hunter 201111 – Discovering miniature inverted-repeat Transposable Elements from Genomic Sequences

MITE-Hunter 201111

:: DESCRIPTION

MITE-Hunter was designed to identify miniature invertedrepeat transposable elements (MITEs) as well as other small (< 2Kb, default) class 2 nonautonomous transposable elements (TEs) from genomic DNA datasets. Class 1 TEs and long TEs can’t be found by MITE-Hunter. TEs with too many mutations and mismatches in the terminal inverted repeats (TIRs) may not be detected.

::DEVELOPER

MITE-Hunter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl
NCBI BLAST
Muscle
mDust

:: DOWNLOAD

MITE-Hunter

:: MORE INFORMATION

Citation

Nucl. Acids Res. (2010) 38 (22): e199.
MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences
Yujun Han and Susan R. Wessler

DRIMust 1.0 – Discovering Ranked Imbalanced Motifs using suffix trees

DRIMust 1.0

:: DESCRIPTION

DRIMUST is a software implementation of a new statistical and algorithmic approach that we developed to enable efficient motif searches, covering a broader range of motif spaces comparing with state of the art motif searching tools. In particular, DRIMUST can efficiently search for variable gapped motifs, long motifs and motifs over large alphabets. The motif structure that DRIMUST searches comprises two half sites separated by a gap, that can be of a variable length.

::DEVELOPER

Yakhini Lab and the Mandel-Gutfreund Lab, at the Technion.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
JRE

:: DOWNLOAD

DRIMust

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W174-9. doi: 10.1093/nar/gkt407. Epub 2013 May 17.
DRIMust: a web server for discovering rank imbalanced motifs using suffix trees.
Leibovich L1, Paz I, Yakhini Z, Mandel-Gutfreund Y.

Limor Leibovich, Zohar Yakhini:
Efficient motif search in ranked lists and applications to variable gap motifs.
Nucl. Acids Res. (2012) 40 (13): 5832-5847.

cn.MOPS 1.32.0 – Mixture Of PoissonS for Discovering Copy Number variations in Next Generation Sequencing data

cn.MOPS 1.32.0

:: DESCRIPTION

cn.MOPS is an algorithm that accurately detects copy number variations in next generation sequencing data in a study of multiple samples.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
R Package
BioConductor

:: DOWNLOAD

cn.MOPS

:: MORE INFORMATION

Citation

Günter Klambauer, Karin Schwarzbauer, Andreas Mayr, Djork-Arné Clevert, Andreas Mitterecker, Ulrich Bodenhofer, Sepp Hochreiter.
“cn.MOPS: mixture of Poissons for discovering copy number variations in next generation sequencing data with a low false discovery rate.”
Nucleic Acids Research 2012 40(2)