Table 2.
Comparison of various Id converters
| Features of mapping services | Gene/Clone ID converter | ID mapping by UniProt | MatchMiner | DAVID gene ID conversion tool | g:Convert | CRONOS | bioDBnet:db2db |
|---|---|---|---|---|---|---|---|
| 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 |
aAll input Id types are potential output Id types as well (eg): as in Id mapping by UniProt. In some cases, however, there are additional output Id types available to choose from which are not available as input Id using that particular converter. Such output Id types are mentioned in parentheses and are indicated as 'additional output' (eg) as in Clone/Gene Id converter, GUI graphical user interface.