No, sorry... I think this is not quite what I want. If I have for example the nt database from NCBI. Then I do a local blastn and I get some results. Now I want to subset the nt databases to the sequences which are in the blastn output... Is this possible?
How to get subset from NCBI databases using Accession/GI
Is there a (nice) way to extract entries from NCBI databases using accession/GI?
Or the Identifier I get when I do a local blastn, like "gi|46392154|gb|AY580535.1|"
So I basically want to get a subset from a NCBI db using a table of identifiers.
1 answer
I assume you are asking to get a subset of sequences. If you have access to preformatted NCBI blast databases you can do so using the blastdbcmd utility that is part of Blast+. An example is here: A: GI chromosome list ncbi. Additional examples here: http://www.ncbi.nlm.nih.gov/books/NBK279689/
In that case you would want to use the blastdb-aliastool from Blast+. Example here: Vertebrate Subset Nr Database? Build My Own? or directly from NCBI: http://www.ncbi.nlm.nih.gov/books/NBK279693/
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