It sounds quite simple but I could not figure out how it is possible to selectively search for gene sequences (say "lanosterol synthase") that were functionally analyzed.
The clue is functionally analyzed sequences are provided with pubmed ID in the genbank.
Even though not all sequences with pubmed ID are not functionally analyzed, most of them are and I could start from there and select the sequences manually.
Additionally, is there a way to enter Entrez filter to blast against the sequences provided with pubmed ID as well?
Is there any way using MESH and Entrez terms to figure this out guys?
EDIT: The question is not about selecting initial query sequence but about limiting the target sequences.
First you can get the set of GenBank access Ids from publications, and then run BLAST from a program to search by BLAST. You may check an example program as follows: https://github.com/biopython/biopython/blob/master/Doc/examples/www_blast.py
Yes, for general Blast we can do that. However in database there are many uncharacterized or predicted/putative genes. My question was not about selecting query sequence but about limiting the target sequences. So my question was/is how to limit the blast or search only among already characterized genes only?
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How about using "UniprotKB/Swiss-Prot"? http://web.expasy.org/docs/swiss-prot_guideline.html You will find it in the database section.
Thank you yamule. Ha! why didn't I think that way?! We can work using Swiss-Prot database.
But still, isn't there any MESH term or entrez keyword or python script to limit the search or blast only among characterized genes/proteins within any database since Swiss-Prot doesn't encompass all of them?
Provided that characterized ones have pubmed IDs while others do not, it seems tantalizingly easy to limit the search/blast. Anyway, thank you again!