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Tools for conversion of IDs in genomics

 
  August, 21 2009 11:48
your information resource in human molecular genetics
 
     
Due to the large number of databases and associated IDs, the conversion of gene identifiers is one of the initial and central steps in many workflows related to genomic data analysis.

There are several freely available ID conversion tools. We present here a list of some of these online servers that allow an automatic processing of large gene lists.

An initial comparison of the output given by some of these tools shows that there are differences in their performances for some ID conversions.

In addition, there are differences in the types of possible inputs and outputs (Ensembl, HGNC, EntrezGene, RefSeq, UniGene, etc) for these tools.

Links

Babelomics ID-Converter

http://babelomics.bioinfo.cipf.es/

Clone/Gene ID Converter

http://idconverter.bioinfo.cnio.es/

DAVID Gene ID Conversion Tool

http://david.abcc.ncifcrf.gov/conversion.jsp

g:Profiler Gene ID Converter

http://biit.cs.ut.ee/gprofiler/gconvert.cgi

ID Converter System

http://biodb.jp/#ids

MatchMiner

http://discover.nci.nih.gov/matchminer/MatchMinerLookup.jsp

A comparison test of the performance of six tools for ID conversion

http://www.scribd.com/doc/18966500/Id-Converters-Test

References:

Alibés A, Yankilevich P, Cañada A, Díaz-Uriarte R. IDconverter and IDClight: conversion and annotation of gene and protein IDs. BMC Bioinformatics. 2007 Jan 10;8:9.

Al-Shahrour F, Minguez P, Tárraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J. BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res. 2006 Jul 1;34:W472-6.

Bussey KJ, Kane D, Sunshine M, Narasimhan S, Nishizuka S, Reinhold WC, Zeeberg B, Ajay W, Weinstein JN. MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol. 2003;4(4):R27

Huang da W, Sherman BT, Stephens R, Baseler MW, Lane HC, Lempicki RA. DAVID gene ID conversion tool. Bioinformation. 2008 Jul 30;2(10):428-30.

Imanishi T, Nakaoka H. Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases. Nucleic Acids Res. 2009 Jul 1;37:W17-22.

Reimand J, Kull M, Peterson H, Hansen J, Vilo J. g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 2007 Jul;35:W193-200.

Diego Forero, MD

Editor, hum-molgen.org


Message posted by: Diego Forero

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