Inquiry of Parsing tblastn result to get nucleotide sequence from the db file

sunfuhui · 09-11-2012, 02:26 PM

Hi all,

I met a problem when I tried to parse tblastn result:

Using either bioperl Bio::SearchIO ($hsp->hit_string) or -outfmt parameter of tblastn can only return the amino acid sequence of the hit.

But I want to get the original nucleotide sequence before translation (not the whole one, but only the part which matches the $hsp->query_string).

How could I do that? Any idea?

Thanks a lot in advance!!!!!!!!!

All the best,
Ying

TiborNagy · 09-12-2012, 02:03 AM

Hi,

tblastn won't give you the nucleotide sequences, however you get the subject start and end positions. You can use an Emboss program (seqret) or Bioperl to get the sequence from the original file.

sunfuhui · 09-12-2012, 05:39 AM

Thank you, TiborNagy!

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09-11-2012, 02:26 PM	#1
sunfuhui Junior Member Location: athens, ga Join Date: Jul 2012 Posts: 8	Inquiry of Parsing tblastn result to get nucleotide sequence from the db file Hi all, I met a problem when I tried to parse tblastn result: Using either bioperl Bio::SearchIO ($hsp->hit_string) or -outfmt parameter of tblastn can only return the amino acid sequence of the hit. But I want to get the original nucleotide sequence before translation (not the whole one, but only the part which matches the $hsp->query_string). How could I do that? Any idea? Thanks a lot in advance!!!!!!!!! All the best, Ying

09-12-2012, 02:03 AM	#2
TiborNagy Senior Member Location: Budapest Join Date: Mar 2010 Posts: 329	Hi, tblastn won't give you the nucleotide sequences, however you get the subject start and end positions. You can use an Emboss program (seqret) or Bioperl to get the sequence from the original file.

09-12-2012, 05:39 AM	#3
sunfuhui Junior Member Location: athens, ga Join Date: Jul 2012 Posts: 8	Thank you, TiborNagy!