I have list of UniProt entries that corresponds to human proteins and I want the list domains composing those proteins. i.e I want the list of domains that exists in the first protein, then the second one, and so on. I found that there are many public databases that provide data about proteins (e.g. Pfam, Uniprot, InterPro, CATH). I am wondering what is the best one? Which one should I rely on while collecting this type of data?
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ahmedmelmoselhy •
I prefer Ensembl. Because of the data integration in Ensembl, you just need to use only one database and one API throughout a project and annotations are then also consistent. Using multiple resources with different notions/definitions/APIs is a pain.
Uniprot and Pfam are great and hand curated. I know less the others.
Thanks. For Pfam and UniProt, if I want to choose one of them, which is better ?
You can upload your list of proteins using the batch retrieve service on the UniProt website (https://www.uniprot.org/uploadlists). Once you have your results, you can customize the layout of the table by adding or removing columns:
Click on "Columns" and then start typing "Pfam" (or "domain", for the UniProt domain annotations) into the search box that appears, and then select the relevant column name.
See also
(video, at about 1min25)
Customise and share your search results: http://insideuniprot.blogspot.com/2015_03_01_archive.html
Actually I really like GeneCards: https://www.genecards.org/
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Define best. Define domains. Each database has its own definition/way of identifying domains.