iRSpot-TNCPseAAC – Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Scid Components

iRSpot-TNCPseAAC

:: DESCRIPTION

The web-server iRSpot-TNCPseAAC was developed for identifying the recombination hotspots and coldspots.

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iRSpot-TNCPseAAC: identify recombination spots with trinucleotide composition and pseudo amino acid components.
Qiu WR, Xiao X, Chou KC.
Int J Mol Sci. 2014 Jan 24;15(2):1746-66. doi: 10.3390/ijms15021746.

SOLAR 7.6.4 – Genetic Variance Components Analysis

SOLAR 7.6.4

:: DESCRIPTION

SOLAR (sequential Oligogenic Linkage Analysis Routines) is an extensive, flexible software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of multiple quantitative traits and/or discrete traits which may involve multiple loci (oligogenic analysis), dominance effects, household effects, and interactions.

::DEVELOPER

Texas Biomed’s Department of Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 SOLAR

:: MORE INFORMATION

Citation

Almasy L, Blangero J (1998)
Multipoint quantitative trait linkage analysis in general pedigrees.
Am J Hum Genet 62:1198-1211.

BioJS 2.0 – A library of JavaScript Components to Represent Biological Data

BioJS 2.0

:: DESCRIPTION

BioJS is an open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers.

::DEVELOPER

BioJS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 BioJS

:: MORE INFORMATION

Citation

BioJS: an open source JavaScript framework for biological data visualization.
Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC.
Bioinformatics. 2013 Apr 15;29(8):1103-4.

COMPADRE 1.2 – COMponent Pathways Analysis of Differential Expression REmoval

COMPADRE 1.2

:: DESCRIPTION

COMPADRE is a web – based tool for detection of differentially expressed pathways.

::DEVELOPER

Cátedra de Bioinformática para el diseño de biomarcadores en genómica computacional

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 COMPADRE

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 15;28(20):2701-2. doi: 10.1093/bioinformatics/bts513. Epub 2012 Aug 24.
COMPADRE: an R and web resource for pathway activity analysis by component decompositions.
Ramos-Rodriguez RR1, Cuevas-Diaz-Duran R, Falciani F, Tamez-Peña JG, Trevino V.

Djeen 1.5.1 – A Joomla! Component to Manage Scientific data

Djeen 1.5.1

:: DESCRIPTION

Djeen (Database for Joomla!’s Extensible Engine) is a Joomla! component to manage an external database and file storing for experimental data. It is a user-friendly application, designed to streamline data storage and annotation collaboratively. Its database model, kept simple, is compliant with most technologies and allows storing and managing of heterogeneous data with the same system. Advanced permissions are managed through different roles.

::DEVELOPER

The CRCM’s Integrative Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • Apach
  • PHP
  • MySQL
  • Joomla!

:: DOWNLOAD

  Djeen

:: MORE INFORMATION

Citation

BMC Res Notes. 2013 Jun 6;6:223. doi: 10.1186/1756-0500-6-223.
Djeen (Database for Joomla!’s Extensible Engine): a research information management system for flexible multi-technology project administration.
Stahl O, Duvergey H, Guille A, Blondin F, Vecchio AD, Finetti P, Granjeaud S, Vigy O, Bidaut G.

NetEffects – Analysing the Effects of Gene Perturbations on Longevity and Components of the Insulin Pathway

NetEffects

:: DESCRIPTION

NetEffects analyse the effects of perturbations to specific pathway components on the rest of the pathway, and especially the biological processes it controls. Two different ways of studying each pathway are provided: querying it by up- or down-regulating specific components, or importing gene expression data and phenotype information (lifespan extension/reduction) and inferring the effects on the pathway.

::DEVELOPER

Thornton group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.
Papatheodorou I, Ziehm M, Wieser D, Alic N, Partridge L, Thornton JM.
PLoS One. 2012;7(12):e50881. doi: 10.1371/journal.pone.0050881

COMPONENT 2.0 – Analysis of Evolutionary Trees

COMPONENT 2.0

:: DESCRIPTION

COMPONENT is a computer program for analysing evolutionary trees and is intended for use in studies of phylogeny, tree shape distribution, gene trees/species trees, host-parasite cospeciation, and biogeography.

::DEVELOPER

Professor Rod Page

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

COMPONENT ; Source Code

:: MORE INFORMATION

For a review of COMPONENT see Joe Slowinski’s review in Cladistics 9: 351-353 (1993).