How to get versioned Protein Accession Number for a Refseq Accession Number?
I have some versioned RefSeq Accession numbers and I would like to know their corresponding Protein Accession Numbers.
According to the RefSeqFAQ http://www.ncbi.nlm.nih.gov/books/NBK50679/#RefSeqFAQ.what_causes_the_version_number there is not a 1-to-1 mapping between these numbers.
Also, nucleotide (NM_, XM_) and protein (NP_, XP) records for the same transcript may not have the same version number after an update. For example, an update to the 5’ UTR of a RefSeq nucleotide record would cause a version number change for the updated nucleotide record but not for the corresponding protein record. Conversely, a change in the annotated start site of the coding sequence without a change in the underlying nucleotide sequence would cause a version number update for the
NP_but not for the
I have tried this, but it gives me a huge
>>> from Bio import Entrez >>> Entrez.email='[email protected]' >>> f = file('entrez_NM_005529.5.txt', 'w') >>> print >>f, Entrez.efetch( ... db="protein",id="NM_005529.5", rettype="native", retmode="xml").read()
The XML results contain the Protein Acc No,
<Textseq-id_accession>NP_005520</Textseq-id_accession> but there is no version specified. Is there a simple way to get obtain the matching protein transcript version?