IDconverter is a tool that converts gene, clone or protein IDs to other IDs. It can be used for small queries or for tens of thousands of IDs (typically from a micro array experiment). Most of the conversions are pregenerated every time that the databases are updated, in order to get a fast answer for each query. Previous versions did not have pregenerated tables, so by using queries of offline pre-generated database we are able to increase speed of response by a factor of up to 20 (most noticeable in queries with many identifiers)
The relations among identifiers is shown in the following Figure:
Regardless of the caveats, please enjoy and let us know your suggestions, comments and complaints.
The input data can be from a single identifiers to several tenths of thousands, and the accepted types of identifiers are Gene Name (HUGO), GenBank accession, UniGene cluster, Ensembl gene, Clone Id, Affymetrix Id, RefSeq_DNA, RefSeq_peptide, EntrezGene, and SwissProt name.
Note: Affymetrix Ids have to be [array] probeset, (i.e., [HG_U133A] 206797_at)
Three different output formats are available:
Patricio Yankilevich created the original version, designed the UI using PHP and the necessary queries to the Ensembl and UniGene databases.
Andreu Alibés upgraded it by adding information on PubMed references, GO terms, several protein identifiers and the UCSC Gene Location. Andreu also created a Python script that pregenerate the conversions to speed up the performance.
Andrés Cañada included Kegg and Reactome to the list of available outputs.
This application is running on a cluster of machines using Debian GNU/Linux as operating system, Apache as web server and MySQL as database server.
NOTE: Due to recent changes on the Ensembl database, Affymetrix IDs for mouse and rat are not available.
Uploaded data set are saved in temporary directories in the server and are accessible through the web until they are erased after some time. Anybody can access those directories, nevertheless the name of the files are not trivial, thus it is not easy for a third person to access your data.
In any case, you should keep in mind that communications between the client (your computer) and the server are not encripted at all, thus it is also possible for somebody else to look at your data while you are uploading or dowloading them.
IDconverter: Alibés, A, et al. (2007) IDconverter and IDClight: Conversion and annotation of gene and protein IDs, BMC Bioinformatics, 8:9 link
Ensembl: E. Birney, et al. (2006) Ensembl 2006, Nucleic Acids Research 34:D556 link
UCSC: A.S. Hinrichs, et al (2006) The UCSC Genome Browser Database: update 2006, Nucleic Acids Research 34:D590 link
NCBI: D.L. Wheeler, et al (2006) Database resources of the National Center for Biotechnology Information, Nucleic Acids Research 34:D173 link
KEGG: M. Kanehisa, et al (2006) From genomics to chemical genomics: new developments in KEGG, Nucleic Acids Research 34:D354 link
Reactome: G. Joshi-Tope, et al (2005) Reactome: a knowledgebase of biological pathways, Nucleic Acids Research 33:D428 link
iHOP: R. Hoffmann, A. Valencia (2004) A gene network for navigating the literature, Nature Genetics 36:664 (2004) link
We thank Robert Hoffmann for helping us link with iHOP.