FuMa – Reporting Overlap in RNA-seq Detected Fusion Genes

FuMa

:: DESCRIPTION

FuMa (Fusion Matcher) is a program that reports identical fusion genes based on gene-name annotations.

::DEVELOPER

FuMa team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 FuMa

:: MORE INFORMATION

Citation

FuMa: reporting overlap in RNA-seq detected fusion genes.
Hoogstrate Y, B?ttcher R, Hiltemann S, van der Spek P, Jenster G, Stubbs AP.
Bioinformatics. 2015 Dec 10. pii: btv721

ROVER 2.0.0 / UNDR ROVER 2.0.0 – Read Overlap Variant Caller

ROVER 2.0.0 / UNDR ROVER 2.0.0

:: DESCRIPTION

ROVER is a read-pair overlap considerate variant-calling software for PCR-based massively parallel sequencing datasets

UNDR ROVER (Unmapped Primer directed read overlap Variant caller) is an improved version of our ROVER variant calling tool for targeted DNA sequencing.

::DEVELOPER

Bernie Pope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 ROVER , UNDR ROVER

:: MORE INFORMATION

Citation:

UNDR ROVER – a fast and accurate variant caller for targeted DNA sequencing.
Park DJ, Li R, Lau E, Georgeson P, Nguyen-Dumont T, Pope BJ.
BMC Bioinformatics. 2016 Apr 16;17(1):165. doi: 10.1186/s12859-016-1014-9.

ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets.
Pope BJ, Nguyen-Dumont T, Hammet F, Park DJ.
Source Code Biol Med. 2014 Jan 24;9(1):3. doi: 10.1186/1751-0473-9-3.

CLUSTOM 0.1.1 – CLUSTering 16S NGS Sequences by Overlap Minimization

CLUSTOM 0.1.1

:: DESCRIPTION

CLUSTOM that is categorized into hierarchical clustering approach is a program for clustering high-throughput 16S sequences with user-defined thresholds.

::DEVELOPER

CLUSTOM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CLUSTOM

:: MORE INFORMATION

Citation

CLUSTOM: a novel method for clustering 16S rRNA next generation sequences by overlap minimization.
Hwang K, Oh J, Kim TK, Kim BK, Yu DS, Hou BK, Caetano-Anollés G, Hong SG, Kim KM.
PLoS One. 2013 May 1;8(5):e62623. doi: 10.1371/journal.pone.0062623

LOLA 1.0.0 – Genomic Locus Overlap Enrichment Analysis

LOLA 1.0.0

:: DESCRIPTION

LOLA (Locus Overlap Analysis) is an R Bioconductor package for genomic locus overlap enrichment. LOLA lets you test your genomic ranges of interest against a database of other genomic range sets to identify enrichment of overlap, tying external annotation to your regions of interest.

::DEVELOPER

Nathan Sheffield

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 LOLA

:: MORE INFORMATION

Citation

LOLA: Enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.
Sheffield NC, Bock C.
Bioinformatics. 2015 Oct 27. pii: btv612.

Dover Analyzer 0.1.2 – Overlap and Diversity in Antimicrobial Peptide Database

Dover Analyzer 0.1.2

:: DESCRIPTION

Dover Analyzer is a wizard like application that takes collections of databases annotated in FASTA format and guides the user through a few steps to compute the overlap, diversity and redundant or non-redundant sets of peptide sequences.

::DEVELOPER

Molecular Biosilico Discovery MultiSystem

:: SCREENSHOTS

DoverAnalyzer

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 Dover Analyzer

:: MORE INFORMATION

Citation

Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences.
Aguilera-Mendoza L, Marrero-Ponce Y, Tellez-Ibarra R, Llorente-Quesada MT, Salgado J, Barigye SJ, Liu J.
Bioinformatics. 2015 Mar 29. pii: btv180.

SeqPrep 1.1 – Tripping Adaptors and/or Merging paired reads with overlap into Single Reads.

SeqPrep 1.1

:: DESCRIPTION

SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap.

:: DEVELOPER

John St. John

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SeqPrep

:: MORE INFORMATION

MIMO 1.0 – Molecular Interaction Maps Overlap

MIMO 1.0

:: DESCRIPTION

MIMO addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information.

::DEVELOPER

Group of Clinical Genomic Networks

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MIMO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 May 15;14:159. doi: 10.1186/1471-2105-14-159.
MIMO: an efficient tool for molecular interaction maps overlap.
Di Lena P1, Wu G, Martelli PL, Casadio R, Nardini C.

overlap – Compute Overlap between two sets of Genomic Features

overlap

:: DESCRIPTION

overlap is a program that computes the overlap between two sets of genomic features. More precisely it takes two gff files of genomic features as input and for each feature of the first set, says whether it is overlapped by a feature of the second set.

::DEVELOPER

Toni Hermoso Pulido

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 overlap

:: MORE INFORMATION

Al-Eigen – Contact Map Overlap by Alignment of Eigenvectors

Al-Eigen

:: DESCRIPTION

Al-Eigen (Alignment of Eigenvectors)  implements a heuristic procedure for computing a solution to the Contact Map Opverlap (CMO) problem. The algorithm uses the standard eigenvalue decomposition of symmetric matrices to obtain a set of principal eigenvectors weighted by the square root of corresponding eigenvalues. The overlap between the two maps is obtained by computing the optimal global alignment between the respective two sets of weighted eigenvectors.

::DEVELOPER

 Bioinformatics group, Department of Computer Science, University of Bologna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 Al-Eigen

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2250-8. Epub 2010 Jul 7.
Fast overlapping of protein contact maps by alignment of eigenvectors.
Di Lena P, Fariselli P, Margara L, Vassura M, Casadio R.