Path 1.1.0 / Path2 0.8 – Pathway-based / Ontology , Genetic Association Analysis

Path 1.1.0 / Path2 0.8

:: DESCRIPTION

Path is designed to help researchers interface bioinformatic information from several online resources with data from genetic association studies. Path is a valuable tool for investigating gene-gene interactions in large genetic association studies. In addition, Path can be used to help store and visualize data from genetic association studies. Path is compatible with LINKAGE pre-makeped data files that are accompanied by standard QTDT data files.

Path2 is designed to conduct pathway-based analyses of Genome-wide association studies (GWASs). Path2 aims to better understand the complex nature of genetic susceptibility to complex diseases by applying pathway-based models using bioinformatics techniques.

::DEVELOPER

Genapha

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows with cygwin/MacOsX
  • Java
  • Perl

:: DOWNLOAD

 Path , Path2

:: MORE INFORMATION

Citation

Zamer, Tripp, Ellis, Daley (2009),
Path: a tool to facilitate pathway-based genetic association analysis“,
Bioinformatics, 25(18):2444-2446.

FMTP – Fingerprint-based Minimal Tiling Path

FMTP v1

:: DESCRIPTION

FMTP is a software tool to compute the MTP of a physical map based purely on restriction fingerprint data (and the contigs). FMTP completely ignores the ordering of clones obtained by the physical map algorithm.

::DEVELOPER

Bozdag Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FMTP

:: MORE INFORMATION

Citation

A graph-theoretical approach to the selection of the minimum tiling path from a physical map.
Bozdag S, Close TJ, Lonardi S.
IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar-Apr;10(2):352-60. doi: 10.1109/TCBB

path 20140624 – Protein Back-translation and Alignment

path 20140624

:: DESCRIPTION

PATH is a tool that addresses the problem of finding distant protein homologies where the divergence is the result of frameshift mutations and substitutions.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX / Linux
  • Java

:: DOWNLOAD

 path

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2010 Jan 4;5(1):6. doi: 10.1186/1748-7188-5-6.
Back-translation for discovering distant protein homologies in the presence of frameshift mutations.
Girdea M, Noe L, Kucherov G.

NetPathMiner 1.22.0 – R package for Network Path Mining through Gene Expression

NetPathMiner 1.22.0

:: DESCRIPTION

NetPathMiner implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats, enabling its utility to most common pathway databases. In addition, NetPathMiner provides different visualization techniques to facilitate the analysis of even thousands of output paths.

::DEVELOPER

NetPathMiner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 NetPathMiner 

:: MORE INFORMATION

Citation

NetPathMiner: R/Bioconductor package for network path mining through gene expression.
Mohamed A, Hancock T, Nguyen CH, Mamitsuka H.
Bioinformatics. 2014 Jul 28. pii: btu501.

cell-motility 2.0 – Analysis of Cell Motility Paths over time

cell-motility 2.0

:: DESCRIPTION

The cell_motility software is an open source Java application under the GNU-GPL license that provides a clear and concise analysis workbench for large amounts of cell motion data. Apart from performing the necessary calculations, the software also visualizes the original motion paths as well as the results of the calculations to help the user interpret the data.

::DEVELOPER

Computational Omics and Systems Biology Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 cell-motility

:: MORE INFORMATION

Citation

Martens et al.
Cell Motility: a cross-platform, open source application for the study of cell motion paths.
BMC Bioinformatics (2006) vol. 7 pp 289