Did NCBI deactivate many RefSeq accession numbers?

Question

[biomarco]

Hi everyone,

I recently updated my local Blast nr database and realized, to my great surprise, that many accession numbers are not there anymore. I initially thought the accession numbers have changed for some reason, but it looks like there were sequences removed.

For instance, this WP_026324618 was a sequence that last year could be found by in the nr database used by Blast. Unfortunately, apparently after the last database update, it can't be found anymore and the closest one has just 77% identity.

I didn't expect something like this to happen and I'm afraid many valuable sequences cannot be found anymore by running Blast searches. I'm really confused... What does the Biostars community think about that?

Answer 1

[GenoMax]

If you visit the page for this record you can see that the reason is listed as

This protein record was suppressed because it is no longer annotated on any genome

If this sequence was determined to be inaccurate or incorrectly annotated one would not want it to stick around for obvious reasons. You could email NCBI help desk and see if they have any additional insight.

As you are probably aware WP* records are a special category.

[biomarco]

Thanks for the heads up on the WP records, I was not aware of its meaning. So it was removed because it is no longer found on any RefSeq genome. It's a pity since the sequence is an active imine reductase reported in literature. I may ask NCBI as you suggested.

Thanks for answering!

[vkkodali_ncbi]

Adding to what GenoMax said... this WP was annotated on https://www.ncbi.nlm.nih.gov/assembly/GCF_000374745.1, sequence NZ_KB895151.1 which has been suppressed by request from the submitter because 'the corresponding paper has not yet been published.' See message on: https://www.ncbi.nlm.nih.gov/nuccore/ARGK00000000.1/

[biomarco]

This is really good to know, thanks a lot for investigating into that!