Question: How to obtain all accession.version identifiers for a BLAST database using ENTREZ
0
gravatar for massa.kassa.sc3na
4 days ago by
massa.kassa.sc3na150 wrote:

Hi all,

background: I need to be able to recognize all possible sequence identifiers present in preformatted NCBI nucleotide databases. I've implemented regular expression following https://www.ncbi.nlm.nih.gov/Sequin/acc.html, but it is not enough. Other accessions (e.g. PDB) are also present. So I would like to have examples of all possible formats I can encounter. But I was not able to find any list which would describe what actually can be inside those databases.

One possible solution, I thought would be to use ENTREZ to retrieve the accessions for me. There is blastdbinfo database which lists the avalible databases. But I not able to get elink to link anywhere.

Lets for example focus on refseq_genomes. The database is available with following command:

esearch -query refseq_genomes[DB] -db blastdbinfo

So given that I want nucleotide sequence accessions present in that database what the elink statement should be?

esearch -query refseq_genomes[DB] -db blastdbinfo | ... SOME ELINK .... | efetch --format acc

For ENTREZ experts here - How do I tell which database links where?

I know I can download the databases and use blastdbcmd to obtain the accessions, but It should be possible to obtain the accessions in some better way.

Thank you

blast entrez elink • 65 views
ADD COMMENTlink modified 4 days ago • written 4 days ago by massa.kassa.sc3na150
1

For a given db, you can find all available link names and a brief description as follows:

einfo -db blastdbinfo

The Entrex Link Descriptions webpage also lists this information but I am not sure how up-to-date that is. It looks like blastdbcmd may be the best solution for you.

ADD REPLYlink written 4 days ago by vkkodali1.4k

Thank you for the link. According to that it looks like there is no direct link between blastdbinfo and e.g. nuccore.

ADD REPLYlink written 4 days ago by massa.kassa.sc3na150
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