Tag: Analysis Tool

SNP2CAPS – SNP and INDEL Analysis Tool for CAPS Marker Development

SNP2CAPS

:: DESCRIPTION

SNP2CAPS facilitates the computational conversion of SNPs into CAPS markers. A simple algorithm involves the screening of multiply-aligned sequences for restriction sites followed by a selection pipeline that allows the deduction of CAPS candidates by the identification of putative alternative restriction sites.

::DEVELOPER

Thomas Thiel  at the IPK-Gatersleben

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Perl

:: DOWNLOAD

 SNP2CAPS

:: MORE INFORMATION

Citation

T. Thiel, R. Kota, I. Grosse, N. Stein, and A. Graner.
SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development.
Nucleic Acids Research, 32(1):e5, 2004.

PathwayLab 1.3 – Pathway Analysis tool

PathwayLab 1.3

:: DESCRIPTION

PathwayLab is an in silico pathway analysis tool, enabling pharmaceutical R&D to reach their target decisions faster and with higher accuracy.

::DEVELOPER

InNetics AB

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • MS Visio 2003 or later.

:: DOWNLOAD

 PathwayLab

:: MORE INFORMATION

Citation

Drug Discov Today. 2010 May;15(9-10):365-70. Epub 2010 Mar 6.
Biochemical modeling with Systems Biology Graphical Notation.
Jansson A, Jirstrand M.

T2 1.3 – Tiling Microarray Analysis Tools

T2 1.3

:: DESCRIPTION

T2 (TiMAT2) contains tools for low and high level genomic tiling microarray analysis using the Affymetrix, NimbleGen, and Agilent platforms. It is designed for processing single and multi chip data sets from ChIP-Chip, RNA difference, and aCGH experiments.

::DEVELOPER

David Nix

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 T2

:: MORE INFORMATION

SAGAT 1.0 – Svd Augmented Gene expression Analysis Tool

SAGAT 1.0

:: DESCRIPTION

SAGAT (SVD Augmented Gene expression Analysis Tool)is an R package enabling the integration of currently existing microarray data from repositories like NCBI’s Gene Expression Omnibus (GEO) with microarray data querying conditions of interest. The goal of this integration is to better identify differentially expressed genes in the query conditions

::DEVELOPER

SAGAT Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SAGAT

:: MORE INFORMATION

Citation

Daigle BJ Jr, Deng A, McLaughlin T, Cushman SW, Cam MC, Reaven G, Tsao PS, Altman RB.
Using pre-existing microarray datasets to increase experimental power: application to insulin resistance.
PLoS Comput Biol. 2010 Mar 26;6(3):e1000718.