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.
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