Question: How to obtain all accession.version identifiers for a BLAST database using ENTREZ
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, 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

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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1225 users visited in the last hour