SAMBLASTER 0.1.22 – Duplicate Marking and Structural Variant Read Extraction

SAMBLASTER 0.1.22

:: DESCRIPTION

samblaster is a tool to mark duplicates and extract discordant and split reads from sam files.

::DEVELOPER

Ira Hall Lab at University of Virginia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SAMBLASTER 

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 7. [Epub ahead of print]
SAMBLASTER: fast duplicate marking and structural variant read extraction.
Faust GG1, Hall IM.

metaRNAmodules 1.0.2 – Automated RNA 3D Module Extraction and Modeling

metaRNAmodules 1.0.2

:: DESCRIPTION

metaRNAmodules is a pipeline which completely automates extracting putative FR3D modules and mapping of such modules to Rfam alignments to obtain comparative evidence.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  metaRNAmodules

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Dec;41(22):9999-10009. doi: 10.1093/nar/gkt795.
Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.
Theis C, Höner Zu Siederdissen C, Hofacker IL, Gorodkin J.

Bubble GUM – Extraction of Phenotype Molecular Signatures and Comprehensive Visualization

Bubble GUM

:: DESCRIPTION

Bubble GUM (GSEA Unlimited Map) is a computational tool that allows to automatically extract phenotype signatures based on transcriptomic data and to perform easily multiple GSEA runs in a row.

::DEVELOPER

Centre d’Immunologie, de Marseille-Luminy

:: SCREENSHOTS

BubbleGUM

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Bubble GUM

:: MORE INFORMATION

Citation

BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses.
Spinelli L, Carpentier S, Montañana Sanchis F, Dalod M, Vu Manh TP.
BMC Genomics. 2015 Oct 19;16(1):814. doi: 10.1186/s12864-015-2012-4.

EDGE 2.2.0 – Extraction of Differential Gene Expression

EDGE 2.2.0

:: DESCRIPTION

EDGE is a software package for the significance analysis of DNA microarray experiments for both standard and time course experiments based on our new Optimal Discovery Procedure and Time Course Methodology

::DEVELOPER

Jeffrey LeekAlan Dabney, Eva Monsen and John Storey.

:: SCREENSHOTS

EDGE

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R
  • BioConductor

:: DOWNLOAD

EDGE

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 15;27(4):509-15. doi: 10.1093/bioinformatics/btq701. Epub 2010 Dec 24.
A computationally efficient modular optimal discovery procedure.
Woo S, Leek JT, Storey JD.

V-Xtractor 2.1 – Extraction of Variable Subregions from SSU or LSU rRNA Sequences

V-Xtractor 2.1

:: DESCRIPTION

V-Xtractor is a Perl-based, high-throughput software tool that locates, verifies, and extracts defined segments of sequence information from sequence datasets. Hidden Markov Models are used to detect the conserved boundaries of the target region and to extract the interjacent sequence information (that is for example the hyper-variable regions of the rRNA gene or the internal transcribed spacer regions of the rRNA operon). This tool extracts phylogenetically comparable regions without prior multiple sequence alignments and improves reliability of the data by confirming basic authenticity of the sequence.

::DEVELOPER

Martin Hartmann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl
  • HMMER

:: DOWNLOAD

  V-Xtractor

:: MORE INFORMATION

Citation:

Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH (2010).
V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences.
Journal of Microbiological Methods 83(2): 250-253.

miRTex – Text Mining System for miRNA-Gene Relation Extraction

miRTex

:: DESCRIPTION

miRTex is a text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature.

::DEVELOPER

Center for Bioinformatics and Computational Biology, University of Delaware

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

miRTex: A Text Mining System for miRNA-Gene Relation Extraction.
Li G, Ross KE, Arighi CN, Peng Y, Wu CH, Vijay-Shanker K.
PLoS Comput Biol. 2015 Sep 25;11(9):e1004391. doi: 10.1371/journal.pcbi.1004391.

ArchTEx 1.0.6 – Accurate Extraction and Visualization of Next-Generation Sequence data

ArchTEx 1.0.6

:: DESCRIPTION

ArchTEx (Architectural Tag Extender) identifies the optimal extension of sequence tags based on the maximum correlation between forward and reverse tags and extracts and visualizes sites of interest using the predicted extension.

::DEVELOPER

Buck Lab

:: SCREENSHOTS

ArchTEx

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 ArchTEx

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Apr 1;28(7):1021-3. doi: 10.1093/bioinformatics/bts063. Epub 2012 Feb 2.
ArchTEx: accurate extraction and visualization of next-generation sequence data.
Lai WK1, Bard JE, Buck MJ.

GFF-Ex 2.3 – Genome Feature Extraction package

GFF-Ex 2.3

:: DESCRIPTION

GFF-Ex, a Genome Feature extraction package extracts Gene, Exon, Intron, Upstream Region of Gene (Promoters), Intergenic and CDS/cDNA sequences by just tweeting in the Genome Feature File (gff) along with the corresponding genome/chromosome sequence.

::DEVELOPER

Bioinformatics Centre ICGEB New Delhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 GFF-Ex

:: MORE INFORMATION

Citation

BMC Res Notes. 2014 May 24;7:315. doi: 10.1186/1756-0500-7-315.
GFF-Ex: a genome feature extraction package.
Rastogi A, Gupta D

MassSpec 1.1 – Peak list Extraction from Proteomic Mass Spectra

MassSpec 1.1

:: DESCRIPTION

MassSpecis a MATLAB implementation of the peak list extraction procedure

::DEVELOPER

laboratorio di Bioinformatica e Biologia Sintetica – Univ. of Pavia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Matlab

:: DOWNLOAD

 MassSpec

:: MORE INFORMATION

Citation

BMC Bioinformatics 2010, 11:518 doi:10.1186/1471-2105-11-518
Accurate peak list extraction from proteomic mass spectra for identification and profiling studies.
Barbarini N, Magni P.

ChExVis – Molecular Channel Extraction and Visualization

ChExVis

:: DESCRIPTION

CHEXVIS is a tool for molecular channel extraction and visualization. CHEXVIS supports the visual exploration of multiple channels together with their geometric and physico-chemical properties thereby enabling the understanding of the basic biology of transport through protein channels

::DEVELOPER

Visualization & Graphics Lab, Dept. of Computer Science & Automation, and Chandra Lab, Dept. of Biochemistry.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CHEXVIS: a tool for molecular channel extraction and visualization
Masood TB, Sandhya S, Chandra N, Natarajan V.
BMC Bioinformatics. 2015 Apr 16;16(1):119.