Question: Getting Blastx Translated Query
0
gravatar for DoubleDecker
7.9 years ago by
DoubleDecker140
United Kingdom
DoubleDecker140 wrote:

I was wondering if there is a way to retrive the translated nucleotide query used to obtain a given hit in blastx? I want to get the translated sequence from my query in the correct frame based on my blastx results.

• 2.9k views
ADD COMMENTlink modified 6.1 years ago by Biostar ♦♦ 20 • written 7.9 years ago by DoubleDecker140
2
gravatar for Damian Kao
7.9 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

You can use biopython/bioperl to retrieve the translation frame of your blast result. Then use that frame to do a translation of your query nucleotide sequence.

Here is how to parse the blast output: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc90

Here is how to do a translation of your nucleotide sequence: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc25

ADD COMMENTlink written 7.9 years ago by Damian Kao15k
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