Translation
Translation services for genes and proteins based on Ensembl
Genes and proteins may be referenced using a variety of identifier formats: Ensembl, Entrez, UniProt, RefSeq, Affy probes, etc. Translating between these names can be time consuming and error prone.
This workflow uses identifier translation files downloaded from Ensembl BioMart to translate gene and protein identifiers between formats. The files are downloaded separatedly for each organism and build, to account for changes overtime that could introduce inconsistencies.
Tasks
The organism input parameter defines the organism and build to use. For instance Homo sapiens is written Hsa, and for the hg18 build you can specify it as Hsa/may2009.
The format is specified using the same text as appears in BioMart. The most important are:
- Ensembl Gene ID
- Associated Gene Name
- UniProt/SwissProt ID
- Entrez Gene ID
The main tasks are: translate, and translate_tsv
- formats Output available identifier formats for a given organism
- transcript_to_protein Translate transcript to their corresponding protein ids
- translate Translate gene ids to a particular format
- translate_from Translate gene ids to a particular format given in another format
- translate_probe Translate probe ids to a particular format
- translate_probe_from Translate probe ids to a particular format given in another format
- translate_protein Translate protein ids to a particular format
- translate_protein_from Translate protein ids to a particular format given in another format
- tsv_translate Translate gene ids to a particular format. Return TSV
- tsv_translate_from Translate gene ids to a particular format given in another format. Return TSV
- tsv_translate_multiple Translate gene ids to a particular format given in another format. Return TSV with multiple results
- tsv_translate_probe Translate probe ids to a particular format. Return TSV
- tsv_translate_probe_from Translate probe ids to a particular format given in another format. Return TSV
- tsv_translate_protein Translate protein ids to a particular format. Return TSV
- tsv_translate_protein_from Translate protein ids to a particular format given in another format. Return TSV
