s. start and s.end in tabular BLAST output are the wrong way around?

Question

[rmartson]

I'm carrying out commandline local BLAST+ using Biopython. The outputfmt = 7 so I get tabular format with comments. I use the BLAST results to extract flanks from either side of the hit later on, so I want to be sure the start and end for the hit I'm using are correct. However, sometimes I get results like this:

54653640 54652673

Where the "s. start" value is higher than the "s. end" value. In these cases I select the second value as the start, but I feel like I'm still having problems later on because of this.

Why are these values the wrong way around for so many hits?

Answer 1

[h.mon]

This is happening because your query is being aligned to the reverse-complemented subject sequence. Why this is happening and the consequences for your downstream analyses will depend on what your sequences and what your downstream analyses are.

[rmartson]

So when retrieving flanks from either side of a reverse-complement hit, is it wrong to simply extract the sequence either side of the hit in the FASTA sequence for that chromosome? Do I need to reverse-complement it too?

[Peter]

If I have understood your question, yes - if you are trying to get the matched sequence from the reference, it would need reverse complementing.

[biomonte]

So when retrieving the reverse-complement hit, would it be correct to use the option "-strand minus" in blastdbcmd and change the order of "s. start" and "s. end" values in the flag "-range" (i.e., for the above example -range 54652673-54653640)?