Question: Building Protein Models From Tblastn Tabular Format
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gravatar for Kamila001
7.7 years ago by
Kamila001120
Kamila001120 wrote:

Hi,

I have done tblastn and now I have a blast tabular output format for proteins. Each hit has this information

queryId, subjectId, percIdentity, alnLength, mismatchCount, gapOpenCount, queryStart, queryEnd, subjectStart, subjectEnd, eVal, bitScore

what i am interested in is that for each of the protein i could extract the subject start and ends and build a complete protein. The problem is the multiple hits or overlapping hits keeping in mind the evalue and percent id. Is there a simple way to extract this information for each protein to build a model protein? Any type of tool or code could help.

If the question is very simple then please guide to the right path.

Thanks in advance

protein blast parsing • 1.2k views
ADD COMMENTlink modified 7.7 years ago by Lars Juhl Jensen11k • written 7.7 years ago by Kamila001120

How do you want to construct a protein sequence when your BLAST result gives you nucleotide matches? What's the whole point of this? I'm a bit confused by the question ;)

ADD REPLYlink written 7.7 years ago by Michael Schubert6.9k

you are right :), so let me explain, blast hits give the nucleotide hits,I want to retrieve those hits for each query protein and then further translate the sequence to protein. Does it answer your quenstion?

ADD REPLYlink written 7.7 years ago by Kamila001120
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