GeneTrail 3.0 – Gene Set Analysis tool / for pre-processing Microarray data

GeneTrail 3.0

:: DESCRIPTION

GeneTrail is a comprehensive and efficient gene set analysis tool that offers a rich functionality and is easy to use.

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2008 Dec 22;9:552. doi: 10.1186/1471-2105-9-552.
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments.
Keller A1, Backes C, Al-Awadhi M, Gerasch A, Küntzer J, Kohlbacher O, Kaufmann M, Lenhof HP.

Backes C, Keller A, Kuentzer J, Kneissl B, Comtesse N, Elnakady YA, Müller R, Meese E, Lenhof HP.
GeneTrail–advanced gene set enrichment analysis.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W186-92.

PlantTFcat – Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool

PlantTFcat

:: DESCRIPTION

PlantTFcat is a high-performance web-based plant transcription factor and transcriptional regulator categorization and analysis tool, designed to identify and categorize TFs and TRs in genome-scale protein or nucleic acid sequences.

::DEVELOPER

The Zhao Bioinformatics Laboratory

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Nov 12;14:321. doi: 10.1186/1471-2105-14-321.
PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool.
Dai X, Sinharoy S, Udvardi M, Zhao PX.

CCAT 3.0 – Control based ChIPSeq Analysis Tools

CCAT 3.0

:: DESCRIPTION

CCAT is a software package for the analysis of ChIP-seq data with negative control.

:: DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

CCAT

:: MORE INFORMATION

Citation

A signal-noise model for significance analysis of ChIP-seq with negative control.
Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK.
Bioinformatics. 2010 May 1;26(9):1199-204

CGAT – Comparative Genome Analysis Tool

CGAT

:: DESCRIPTION

CGAT is a Comparative Genome Analysis Tool that was depeloped for detailed comparison of closely related bacterial-sized genomes. CGAT visualizes precomputed pairwise genome alignments on both dotplot and alignment viewers. Users can put several information on this alignment, such as existence of tandem repeats or interspersed repetitive sequences and changes in codon usage bias, to facilitate interpretation of the observed genomic changes.

::DEVELOPER

Ikuo Uchiyama (uchiyama@nibb.ac.jp)

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows/ MacOsX
Java

:: DOWNLOAD

CGAT

:: MORE INFORMATION

Citation

CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes.
Uchiyama I, Higuchi T, Kobayashi I.
BMC Bioinformatics. 2006 Oct 24;7:472.

RNAMute / XRNAmute – RNA Secondary Structure Mutation Analysis Tool

RNAMute / XRNAmute

:: DESCRIPTION

RNAmute is an application that provides a user friendly interface for analyzing the effects of point mutations on RNAs secondary structure.

XRNAmute is RNAmute web server for the mutational analysis of RNA secondary structures.

::DEVELOPER

A.Churkin and D. Barash (dbarash@cs.bgu.ac.il)

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Mac / Windows
Java

:: DOWNLOAD

RNAMute

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W92-9. doi: 10.1093/nar/gkr207. Epub 2011 Apr 7.
The RNAmute web server for the mutational analysis of RNA secondary structures.
Churkin A1, Gabdank I, Barash D.

A.Churkin and D. Barash,
“RNAMute: RNA Secondary Structure Mutation Analysis Tool,”
BMC Bioinformatics, 7:221, 2006.

CMAT 0.3.2 – Correlated Mutation Analysis Tool

CMAT 0.3.2

:: DESCRIPTION

The CMAT is a fully automated and reliable web-server for correlated mutation analysis. CMAT automatically performs all the processes for correlated mutation analysis including homology search, multiple sequence alignment construction, sequence redundancy treatment, and various correlated mutation score measures.

:: DEVELOPER

Bioinformatics and Computational Biology Laboratoty,Korea Advanced Institute of Science and Technology (KAIST).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CMAT

:: MORE INFORMATION

Citation

Protein Eng Des Sel. 2012 Nov;25(11):705-13. doi: 10.1093/protein/gzs081. Epub 2012 Oct 16.
Reliable and robust detection of coevolving protein residues.
Jeong CS, Kim D.

SimRare – Rare Variant Simulation and Analysis tool

SimRare

:: DESCRIPTION

SimRare is a program to generate and analyze sequence-based data for rare variant association studies of quantitative and qualitative traits

::DEVELOPER

Center for Statistical Genetics, Baylor College of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX

:: DOWNLOAD

SimRare

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 15;28(20):2703-4. doi: 10.1093/bioinformatics/bts499. Epub 2012 Aug 22.
SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits.
Li B, Wang G, Leal SM.

BINAT 1.0 – Biological Networks Analysis Tool

BINAT 1.0

:: DESCRIPTION

BiNAT is a Java plugin for Cytoscape, an open source bioinformatics software platform for analysis and visualizing molecular interaction networks.

::DEVELOPER

DMB (Data Mining Big) Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX/ android
java
Cytoscape

:: DOWNLOAD

BiNAT

:: MORE INFORMATION

GEMAT 2.0 – Genomics Experiment Management and Analysis Tool

GEMAT 2.0

:: DESCRIPTION

GEMAT is an information management system designed as client-server tool for handling variety of microarray platform eg., Affymetrix GeneChip information. It has builtin analytical tools for performing data mining and posting microarry data to endusers.

::DEVELOPER

Bioinformatics Group, Roskamp Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

LAMPP (Linux-Apache-MySQL-Perl/PHP) environment

:: DOWNLOAD

GEMAT

:: MORE INFORMATION

Citation

Venkatarajan Mathura, Deepak Kolippakkam, Fiona Crawford, Michael Mullan., 2005
“GEMAT: Genomic Experiment Management and Analysis Tool”,
ISMB 2005

L2L 1.2 – Microarray Analysis Tool

L2L 1.2

:: DESCRIPTION

L2L is a simple but powerful tool for discovering the hidden biological significance in microarray data. Through an easy-to-use web interface, L2L will mine a list of up- or down-regulated genes for Gene Ontology terms that are significantly enriched. L2L can also compare the list of genes to a database of hundreds of published microarray experiments, in order to identify common patterns of gene regulation. A downloadable command-line version can run customized and batch analyses.

::DEVELOPER

John Newman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows /MacOsX
perl

:: DOWNLOAD

L2L

:: MORE INFORMATION

Citation

John C Newman and Alan M Weiner
L2L: a simple tool for discovering the hidden significance in microarray expression data
Genome Biology 2005, 6:R81