Table 2 Comparison of various Id converters

Interface

Web-based GUI form

Web-based GUI form

Web-based GUI form, command line

Web-based GUI form

Web-based GUI form

Web-based GUI form

Web-based GUI form

Output format

Html, text, spreadsheet

Html, text

Html, text, spreadsheet

Html, text, spreadsheet

Html, text, spreadsheet, minimal (no header)

Html, email for batch mode

Text, spreadsheet

Organisms

Human, mouse, rat

Human, mouse, rat and many other species

Human, mouse

Human, about another 90,000 species

Human, mouse, rat and 31 other Ensembl-supported genome species

Human, mouse, rat, cow, dog, and fruit fly

A specified list could not be found

Input/output clone or transcript

Clone Ids, Affymetrix Ids, GenBank Accession (Additional output: EMBL)*

GenBank, EMBL, DDBJ

Affymetrix Ids, GenBank Accession, EST, IMAGE Clone Id, FISH-mapped BAC Clone Id

Affymetrix Id, Agilent Id, Illumina Id, GenBank Accession, Gene symbol, GenPept Accession, NCBI GI, RefSeq RNA/Genomic accession

Affymetrix, Agilent, CCDS Ids, Ensembl transcript, Illumina, RefSeq DNA/Genomic

Ensembl/FlyBase Transcript ID, EMBL, Affymetrix, Agilent, CCDS

Affymetrix, Agilent, GenBank, RefSeq Genomic, RefSeq Nucleotide

Input/output gene

HUGO gene names, Entrez gene Ids, Ensembl gene Ids, UniGene cluster Ids, RefSeq RNAs (Additional output: CCDS)^a

Entrez Gene, HGNC, Ensembl, UniGene, TIGR (JCVI)

Gene Symbol HUGO/Alias, Name, UniGene Cluster Id, Entrez Gene Id, RefSeq RNA

Entrez gene Id, Ensembl gene/transcript Id, RefSeq mRNA accession, UniGene Id

Ensembl Gene, Entrez Gene, RefSeq mrna, UniGene

Gene Name, Ensembl/FlyBase Gene ID, GI, GeneID, HGNC, RefSeq mRNA

Entrez Gene ID, Ensembl Gene ID, UniGene

Input/output protein

RefSeq peptides, SwissProt names (Additional output: IPI, PDB)*

UniProtKB, RefSeq, GenPept, IPI, PDB

RefSeq protein

PIR accession, PIR Id, PIR NREF Id, RefSeq Protein accession, Uniprot Id/accession, UniRef Id

Ensembl Protein, IPI, PDB, RefSeq Protein

Protein Name, UniProt, Ensembl/FlyBase Protein ID, IPI, PIR

UniProt Accession, Ensembl Protein ID, GenPept, RefSeq Protein, UniProt

Input/output other information

(Additional output: PubMed, GO, KEGG, Reactome, Chromosomal locations from Ensembl, UCSC Genome Browser, OMIM)^a

SGD, GeneRif, NCBI Taxon, and others

Cytogenetic location: UCSC (Additional output: PubMed, GO, KEGG, Reactome, Chromosomal locations from Ensembl, UCSC Genome Browser, OMIM)*

"Not sure" type also accepted, and many other secondary database identifiers also supported

UCSC, PubMed, GO and many other secondary databases

dbSNP, UniSTS, MGI, orfnames, MIM, MORBID, CDD

GO, InterPro, Biocarta, KEGG, dbSNP, H-Invitational (H-Inv), HomoloGene, MGC, MIM, UniSTS, Taxon, and other secondary databases