Matching protein IDs starting with WP_ to protein IDs starting with YP_

Question

[bio_student]

Hi all,

I have annotated genomes where all CDS have protein IDs starting with YP (e.g., YP_005225157.1). Is there a way to automatically convert protein IDs that start with YP to those starting with WP, without the need to search for them manually in the database?

Thank you.

[Pierre Lindenbaum]

what is

those starting with WP

[bio_student]

For example, I have protein ID: YP_005229578.1 and identical proteins have ID: WP_004151534.1 (see: https://www.ncbi.nlm.nih.gov/ipg/YP_005229578.1). So I would like to somehow match identical proteins which have two protein IDs - YP and WP.

Answer 1

[GenoMax]

Using EntrezDirect:

$ esearch -db ipg -query "YP_005225157" | esummary | xtract -pattern DocumentSummary -element Accession
WP_002888811.1

$ esearch -db ipg -query "YP_005229578" | esummary | xtract -pattern DocumentSummary -element Accession
WP_004151534.1

[bio_student]

This will help. Thank you!!