convert mitochondrial refseq peptide id's (YP_XX) using biomaRt

Question

[glocke01]

I downloaded human.1.protein.faa.gz ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/, which includes protein sequences for mitochrondrial proteins such as this:

>gi|251831107|ref|YP_003024026.1| NADH dehydrogenase subunit 1 (mitochondrion) [Homo sapiens]
MPMANLLLLIVPILIAMAFLMLTERKILGYMQLRKGPNVVGPYGLLQPFADAMKLFTKEPLKPATSTITLYITAPTLALT
IALLLWTPLPMPNPLVNLNLGLLFILATSSLAVYSILWSGWASNSNYALIGALRAVAQTISYEVTLAIILLSTLLMSGSF
NLSTLITTQEHLWLLLPSWPLAMMWFISTLAETNRTPFDLAEGESELVSGFNIEYAAGPFALFFMAEYTNIIMMNTLTTT
IFLGTTYDALSPELYTTYFVTKTLLLTSLFLWIRTAYPRFRYDQLMHLLWKNFLPLTLALLMWYVSMPITISSIPPQT

The difficulty is that I can't get biomaRt to recognize the id YP_003024026. human.1.protein.faa includes refseq ids like NP_12345, which biomaRt recognizes as "refseq_peptide", and XP_12345, which biomaRt recognizes as "refseq_peptide_predicted". I can't figure out how to get it to recognize the YP sequences. I want to find the corresponding entrez id.

In the meantime, there are only 13 YP_1234, so I've solved this problem "by hand" using http://www.ncbi.nlm.nih.gov/protein/YP_003024026 and looking down to find the GeneID. I'd prefer to do it "the right way" in case the id's change in the future.

any advice?

Answer 1

[Denise CS]

Believe it or not, but YP does get recognised as RefSeq Protein ID. I've just tried it and it worked beautifully using the web interface of Ensembl Biomart. Use YP_003024026 instead of YP_003024026.1 and choose your filters as RefSeq protein ID(s). You can have a mix bag of NPs and YPs in your filters and it will work just as well.

[Denise CS]

YP seems to be another example of curated RefSeq protein according to this README. So that explains why we should use RefSeq Protein ID in BioMart as YP = NP but not XP (predicted protein).