Question: Is it possible that sequence have blast hit in arabidopsis database and no blast hit for viridiplantae and swissprot database?
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gravatar for tcf.hcdg
3.4 years ago by
tcf.hcdg60
European Union
tcf.hcdg60 wrote:

I was doing command line blast for around 40000 sequences. I downloaded the protein databases for Arabidopsis thaliana, viridiplantae and swissprot. Then I did the blastp against all these databases.  I found that 46 sequences have no blast hit against Arabidopsis database 96 sequence for viridiplantae and 159 sequences for swissprot database.  

I wonder how the no of sequences has increased in viridiplantae  from 46 to 96 while it contains all the proteins of plants including the Arabidopsis proteins and similarly these numbers increased in swissprot  from 96 to 159 while swissprot contains all the proteins including the viridiplantae.

Now the question is how it is possible that a sequence have blast hit in the Arabidopsis database and the same sequence have no blast hit in viridiplantae and swissprot database.

Is there something wrong with the blast? 

blast • 1.2k views
ADD COMMENTlink modified 3.4 years ago by Michael Dondrup45k • written 3.4 years ago by tcf.hcdg60
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gravatar for Michael Dondrup
3.4 years ago by
Bergen, Norway
Michael Dondrup45k wrote:

Was your E-value cutoff the same for all searches? If so, that would explain the result, given that viridiplantae db really contains all arabidopsis proteins. Larger database yields larger E-values, and thereby fewer significant hits at the same e-value cutoff.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Michael Dondrup45k
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@tcf.hcdg: and note that BLAST always has e-Value cutoff set! It defaults to 10 which is a very bad hit. I just say this to prevent you from writing a statement like "I do not have a cutoff". ;-)

@michael: i think you missed "cutoff" at the end of "... and thereby fewer significant hits at the same e-value"

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Manuel Landesfeind1.2k

thanx, fixed

ADD REPLYlink written 3.4 years ago by Michael Dondrup45k

Thank you! I did not meant to be picky but people frequently get confused when talking/reading about p/e-Values. Therefore, I like it to be precise ;-)

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Manuel Landesfeind1.2k

Yes in all theree cases I have the same cutoff value and same parameters for blast. 

ADD REPLYlink written 3.4 years ago by tcf.hcdg60

Did you had a look at the "unmatched" sequences? How good do they match when blasting against the Ath database?

ADD REPLYlink written 3.4 years ago by Manuel Landesfeind1.2k
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