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.

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.

EDGE 2.22.0 – Extraction of Differential Gene Expression

EDGE 2.22.0

:: 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 Leek, Alan Dabney, Eva Monsen and John Storey.

:: SCREENSHOTS

:: 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.

ACME v1 – Efficient Parallel Motif Extraction from Very Long Sequences

ACME v1

:: DESCRIPTION

ACME (Advanced parallel motif extractor) is an advanced parallel motif extractor. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution.

::DEVELOPER

InfoCloud Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Compiler

:: DOWNLOAD

 ACME

:: MORE INFORMATION

Citation:

Majed Sahli, Essam Mansour, Panos Kalnis:
ACME: Efficient Parallel Motif Extraction from Very Long Sequences.
Technical Report

ITSx 1.1.3 – Extraction of ITS1 and ITS2 from Ribosomal ITS Sequences

ITSx 1.1.3

:: DESCRIPTION

ITSx is a software tool for detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing.

::DEVELOPER

The Bengtsson-Palme Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 ITSx

:: MORE INFORMATION

Citation:

ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing
Johan Bengtsson-Palme, Vilmar Veldre, Martin Ryberg, Martin Hartmann, Sara Branco, Zheng Wang, Anna Godhe, Yann Bertrand, Pierre De Wit, Marisol Sanchez, Ingo Ebersberger, Kemal Sanli, Filipe de Souza, Erik Kristiansson, Kessy Abarenkov, K. Martin Eriksson, R. Henrik Nilsson
Methods in Ecology and Evolution, 2013

XSTREAM – Variable Sequence Tandem Repeats Extraction and Architecture Modeling

XSTREAM

:: DESCRIPTION

XSTREAM is a rapid and powerful algorithm for identifying perfect and degenerate tandem repeat motifs in protein (and nucleotide) sequence data. XSTREAM also effectively models the architecture of repetitive domains in tandem repeat proteins and eliminates motif redundancy to identify “fundamental” tandem repeat patterns.

::DEVELOPER

Newman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Oct 11;8:382.
XSTREAM: a practical algorithm for identification and architecture modeling of tandem repeats in protein sequences.
Newman AM, Cooper JB.

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.

MoTeX – a Word-based HPC tool for MoTif eXtraction

MoTeX

:: DESCRIPTION

MoTeX is an accurate and efficient tool for MoTif eXtraction.

:: DEVELOPER

Dr. Solon P. Pissis

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  •  Linux
  • C Compiler

:: DOWNLOAD

 MoTeX

:: MORE INFORMATION

Citation

Solon P. Pissis, Alexandros Stamatakis, and Pavlos Pavlides.
MoTeX: a word-based HPC tool for MoTif eXtraction.
the Fourth ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2013), pp. 13-22, 2013. ACM Digital Library

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.

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

:: 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.