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

cgta

:: 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.

GATK 3.8-0 – Analysis Tools for Next-generation DNA Sequencers

GATK 3.8-0

:: DESCRIPTION

GATK (The Genome Analysis Toolkit) is a structured programming framework designed to enable the rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce. Since the GATK’s traversal engine encapsulates the complexity of efficiently accessing the next-generation sequencing data, researchers and developers are free to focus on their specific analysis algorithms. This not only vastly improves the productivity of developers, who can quickly write new analyses, but also results in tools that are efficient and robust, and can benefit from improvements to a common data management engine.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

GATK

:: MORE INFORMATION

Citation

Depristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ.
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Nature Genetics 43, 491–498 (2011) doi:10.1038/ng.806

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

GeneTrail / GeneTrailExpress

:: DESCRIPTION

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

GeneTrailExpress provides comprehensive normalization and scoring functions for pre-processing microarray data. The processed data is directly passed to GeneTrail for statistical evaluation in an extensive gene set analysis.

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: 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.

ESTate 0.5 – Expressed Sequence Tag Analysis Tools Etc

ESTate 0.5

:: DESCRIPTION

ESTate (Expressed Sequence Tag Analysis Tools Etc) is a package for EST analysis.

::DEVELOPER

Guy Slater (gslater@hgmp.mrc.ac.uk)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Mac OsX/ Linux
  • C Complier

:: DOWNLOAD

  ESTate

:: MORE INFORMATION

CLUSTERnGO v0.30 – Gene Expression Analysis Tool

CLUSTERnGO v0.30

:: DESCRIPTION

CnG (CLUSTERnGO) is a gene expression analysis tool that clusters gene (or protein) expression profiles, and extracts their GO enrichments.

::DEVELOPER

CnG team

:: SCREENSHOTS

CnG

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • QT

:: DOWNLOAD

 CnG

:: MORE INFORMATION

Citation

CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data.
Fidaner IB, Cankorur-Cetinkaya A, Dikicioglu D, Kirdar B, Cemgil AT, Oliver SG.
Bioinformatics. 2015 Sep 26. pii: btv532.

FX 2.7.1 – RNA-Seq analysis tool on the Cloud

FX 2.7.1

:: DESCRIPTION

FX is a user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing. With FX, you can simply upload your RNA-Seq raw FASTQ data on the cloud, and let the computing infra to do the heavy analysis.

::DEVELOPER

Genomic Medicine Institute, Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FX

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Mar 1;28(5):721-3. doi: 10.1093/bioinformatics/bts023. Epub 2012 Jan 17.
FX: an RNA-Seq analysis tool on the cloud.
Hong D1, Rhie A, Park SS, Lee J, Ju YS, Kim S, Yu SB, Bleazard T, Park HS, Rhee H, Chong H, Yang KS, Lee YS, Kim IH, Lee JS, Kim JI, Seo JS.

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

 NO

:: 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.

Encore 1.1 – GWAS and Biological Data Analysis tool

Encore 1.1

:: DESCRIPTION

Encore is a free, open-source command-line tool for analysis of GWAS (SNP) and other types of biological data.

::DEVELOPER

Insilico Research Group (McKinney Laboratory for Bioinformatics and In Silico Modeling)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Encore

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Sep;37(6):614-21. doi: 10.1002/gepi.21739. Epub 2013 Jun 5.
Encore: Genetic Association Interaction Network centrality pipeline and application to SLE exome data.
Davis NA1, Lareau CA, White BC, Pandey A, Wiley G, Montgomery CG, Gaffney PM, McKinney BA.

csnpAnalysis 1.03 – PANTHER Coding SNP Analysis tool

csnpAnalysis 1.03

:: DESCRIPTION

 csnpAnalysis is a software to estimate the likelihood that a particular nonsynonymous (amino-acid changing) coding SNP will cause a functional impact to the protein.

::DEVELOPER

Paul D. Thomas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 csnpAnalysis

:: MORE INFORMATION

Citation

Paul D. Thomas, et al. 2006.
Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.
Nucl. Acids Res.34: W645-W650.