JEnsemb 1.78 – Java API to Ensembl data systems

JEnsemb 1.78

:: DESCRIPTION

The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources.

::DEVELOPER

Roslin Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX / Windows
Java

:: DOWNLOAD

JEnsemb

:: MORE INFORMATION

Citation

JEnsembl: a version-aware Java API to Ensembl data systems.
Paterson T, Law A.
Bioinformatics. 2012 Nov 1;28(21):2724-31. doi: 10.1093/bioinformatics/bts525.

EASER 1.7.0 – Ensembl Easy Sequence Retriever

EASER 1.7.0

:: DESCRIPTION

EASER is a python program based in PyCogent library for the homology-based retrieval of several sequence data types from Ensembl.

::DEVELOPER

EASER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
Perl

:: DOWNLOAD

EASER

:: MORE INFORMATION

Citation

Emanuel Maldonado, Imran Khan, Siby Philip, Vítor Vasconcelos and Agostinho Antunes
EASER: Ensembl Easy Sequence Retriever
Evolutionary Bioinformatics (2013) 9: 487-490.DOI:10.4137/EBO.S11335

pubmed2ensembl – Link Publications in PubMed to Genes in Ensembl

pubmed2ensembl

:: DESCRIPTION

pubmed2ensembl is an extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species.

::DEVELOPER

the Nenadic group & the Bergman lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Perl
Java
BioMart

:: DOWNLOAD

pubmed2ensembl

:: MORE INFORMATION

Citation

PLoS One. 2011;6(9):e24716. Epub 2011 Sep 29.
pubmed2ensembl: a resource for mining the biological literature on genes.
Baran J, Gerner M, Haeussler M, Nenadic G, Bergman CM.