Question: Problems with accessing the Swissprot database using qblast
gravatar for bondserv
5.3 years ago by
United States
bondserv0 wrote:

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 no results swissprot • 1.4k views
ADD COMMENTlink modified 4.0 years ago by anetth0 • written 5.3 years ago by bondserv0
gravatar for anetth
4.0 years ago by
anetth0 wrote:

Pretty late, but for anybody else:

Try "swissprot" instead of "sp".

ADD COMMENTlink written 4.0 years ago by anetth0
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