Problems with accessing the Swissprot database using qblast
Entering edit mode
8.2 years ago
bondserv • 0

Hello I am part of a project that involved searching for the several proteins across several different species. At this point I have a list of proteins that I am trying to find in other species besides human, particularly zebrafish, mouse, rat, and yeast. My current strategy is to blast these proteins against the Swissprot database in order to find these proteins in other species. However, when I use qblast against Swissprot I do not get anything interesting, but when I blast against the NR database I get results. Every other parameter is the same.

>>> blast = NCBIWWW.qblast("blastp","sp",74760014,hitlist_size=100,gapcosts="11 1",threshold = 11,composition_based_statistics=2,word_size=3,db_genetic_code=1

^Fails to give any hits

>>>blast = NCBIWWW.qblast("blastp","nr",74760014,hitlist_size=100,gapcosts="11 1",threshold = 11,composition_based_statistics=2,word_size=3,db_genetic_code=1)

^Plenty of hits

Is there any explanation for why this could be? When I use BLAST on NCBI I get results that make sense from both Swissprot and NR. Any help I could get would be much appreciated.

qblast swissprot no results • 2.0k views
Entering edit mode
6.9 years ago
anetth • 0

Pretty late, but for anybody else:

Try "swissprot" instead of "sp".


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