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MAdb - This is a tool to retrieve ortholog gene data from our MAdb
MAdb - Mammalian Annotation Database
What is it?
This database contains ensembl_compara, blastn, and gene symbol comparisons of the following species:- Human (Homo sapiens)
- Cow (Bos taurus)
- Pig (Sus scrofa)
- Horse (Equus caballus)
- Rabbit (Oryctolagus cuniculus)
- Mouse (Mus musculus)
- Dog (Canis familiaris)
Database sources and versions:
| Species | Ensembl Compara | BLASTn comparison | GeneSymbol match | |||
|---|---|---|---|---|---|---|
| release_90 | release_95 | 2017-11-24 | 2019-01-10 | 2018-05-22 | 2019-01-10 | |
| Human (Homo sapiens) | GRCh38.p12 | GRCh38.p12 | GRCh38.p12 | GRCh38.p12 | GRCh38.p12 | GRCh38.p12 |
| Cow (Bos taurus) | UMD3.1.1 | ARS-UCD1.2 | UMD3.1.1 | ARS-UCD1.2 | UMD3.1.1 | ARS-UCD1.2 |
| Pig (Sus Scrofa) | Sscrofa11.1 | Sscrofa11.1 | Sscrofa11.1 | Sscrofa11.1 | Sscrofa11.1 | Sscrofa11.1 |
| Horse (Equus caballus) | EquCab2.0 | EquCab3.0 | EquCab2.0 | EquCab3.0 | EquCab2.0 | EquCab3.0 |
| Rabbit (Oryctolagus cuniculus) | OryCun2.0 | OryCun2.0 | OryCun2.0 | OryCun2.0 | OryCun2.0 | OryCun2.0 |
| Mouse (Mus musculus) | GRCm38.p6 | GRCm38.p6 | GRCm38.p6 | GRCm38.p6 | GRCm38.p6 | GRCm38.p6 |
| Dog (Canis familiaris) | CanFam3.1 | CanFam3.1 | CanFam3.1 | CanFam3.1 | CanFam3.1 | CanFam3.1 |
Other database versions:
How to run it?
There are two option to get data out the MAdb. Option one is to select one of the given species and option two is to select a list of IDs. This ID list can only contain one of the following ID types at ones:- EntrezGeneID from NCBI
- Gene Symbol (official HGNC Symbol)
- Ensembl gene ID from Ensembl
- RefSeq (NCBI RNA Accession) [coming soon]
- Run gene IDs (list) only with "GeneSymbol match"
- For the remaining gene IDs run "Ensembl Compara" and check manually on duplicates (most-likely the first hit is the correct hit), delete unclear duplicates, or remove all duplicates
- For the remaining gene IDs run "BLASTn comparison" and check again on duplicates
If you use MADb in your work, please consider citing:
Jochen T Bick, Shuqin Zeng, Mark D Robinson, Susanne E Ulbrich, Stefan Bauersachs, Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms, Database, Volume 2019, 2019, baz086, https://doi.org/10.1093/database/baz086.
Jochen T Bick, Shuqin Zeng, Mark D Robinson, Susanne E Ulbrich, Stefan Bauersachs, Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms, Database, Volume 2019, 2019, baz086, https://doi.org/10.1093/database/baz086.