Console BLAST search in WGS/TSA databases

Question

[NK]

Dear all,

is it possible to use BLAST from the command line to search in multiple remote wgs/tsa NCBI databases?

I need to search for the sequences of exact group of organisms in as many metagenomic wgs/tsa projects as possible and think about how to automate this process.

Thank you very much!

Answer 1

[GenoMax]

Every preformatted/web blast+ database is not available for remote search on the command line. A quick check shows that wgs or tsa are not a valid option for -remote search.

[NK]

Thank you, but I have already checked it. Is there other console option for search in these databases?

[GenoMax]

As far as I know no. You will need to download the sequences and create databases locally.

How can we download all TSA and WGS from NCBI Trace by taxon programmatically? is an older thread but you should get an idea.