I want to find a database(s) or a method where I can find and bulk download all the rabbit MHC genes and domain annotation.
In humans using Ensembl, all MHC genes have names and domains but in the Ensembl rabbit genome they do not.
Therefore:
1. How to find the MHC genes of rabbits? How can I bulk download all the rabbit MHC genes?
2. How to find a database which has all MHC rabbit domain annotations? How can I bulk download all MHC rabbit domain annotations?
3. How can I be sure that I have found all MHC rabbit genes and all MHC rabbit domain using a bioinformatics approach? Which bioinformatics approach should I use?
Any help on methods done this on rabbits or other jawed vertebrates would be greatly appreciated.
Hi Marina
maybe using the UCSC website you'll find the answers (http://genome.ucsc.edu). go to the genomes and select rabbit and your genes. in addition to what you'll see, the genome browser, there is lot of tools including a table browser with which you'll get in text files what you see.
stay safe
fred
Hello Marina,
I think I would use UniProt (https://www.uniprot.org/), filtering by GO terms and species. For example:
goa:("MHC class II protein complex [42613]") AND organism:"Oryctolagus cuniculus (Rabbit) [9986]" --> This would give you all the proteins annotated as being part of MHC class II (with their corresponding gene names and domains).
goa:("MHC class I protein complex [42612]") AND organism:"Oryctolagus cuniculus (Rabbit) [9986]" --> This would give you all the proteins annotated as being part of MHC class I.
In order to bulk download those results you should just click "Download" and in format choose "Text". That way you will have the information concerning the domains and crossreferences to GeneBank and Ensembl to check for the genes and mRNA information.
In case some of the protein text files have no annotation concerning domains, you can query databases such as InterPro (https://www.ebi.ac.uk/interpro/) or PROSITE (https://prosite.expasy.org/) to complete the annotation.
That is the simple answer. For a more complex bioinformatic approach you could just proceed the same with better studied species such as Homo sapiens and Mus musculus. However, instead of downloading their "Text", you could download their FASTA files and perform tblast queries against the rabbit genome or even WGS data from rabbits. That way you could identify potential genes (and/or pseudogenes) not annotated in the current Oryctolagus cuniculus genome draft.
Good hunting!
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