What does sframe signify in BLAST output?

Question

[Vivek]

Hi,

I am relatively new to the field of Bioinformatics and have just been introduced to BLAST. I'm trying to understand the output available from the BLAST program. As listed in the NCBI manual, I am generating output using -outfmt 5 which is an XML output. The <hsp> tag contains the value qframe and hframe.

In case of blastn, these values are 1,-1 which I guess reflects the strandedness of the alignments. However in case of tblastx, the hframe values are often 3,-2 and so on. What does this mean?

Answer 1

[Pierre Lindenbaum]

blastx compares a nucleotide query sequence (2 frames: 1/-1 for strand+ and strand - of DNA) translated in all reading frames against a protein sequence(6 frames (3 frames per strand ): -3/-2/-1/1/2/3 )