How to find gene ids for Pfam ids?

Question

[WUSCHEL]

How to get gene ids for Pfam ids? For a long list of Pfam ids from Arabidopsis thaliana.

Any tool available?

[Pierre Lindenbaum]

you got answers for your previous questions. Validate or comment them please.

• What does PCA really tells about Biological data?
• How to get a list of genes information for a pathway?
• How to extract FASTA headers in R
• etc...

Answer 1

[GenoMax]

Proteome page for Arabidopsis from UniProt: https://www.uniprot.org/uniprotkb?query=proteome:UP000006548

Click on Customize columns --> External Resources --> Families and Domains --> Pfam. Customize anything else you need. Download the entire table. Parse as needed.

[WUSCHEL]

This is fantastic. Thanks a heap.

Answer 2

[dthorbur]

If you're using ensmebl gene IDs, you can use BioMart to download a table with those details. You can also run the sequences through InterProScan.

[WUSCHEL]

Thank you. I donot have ensmebl ids.