I am new to the field of Bioinformatics. I was looking at a BLAST xml output file and I was trying to understand why there are multiple HSPs under each blast hit. I know HSP stands for High-Scoring Segment Pair but I don't really understand how and why multiple HSPs gets assigned to a single hit.
what is the meaning of multiple HSPs under a single hit?
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Okk, so I am giving you a general idea. For instance, for sequence A and sequence B, multiple portions of the sequence might be identical/similar or high scores. To be more specific:
Sequence A: #######AAAAAA????????ATCG///////////////////////////////
Sequence B: #######CCCCCC????????ATCG///////////////////////////////
So, you will get three results for the above two sequences. One for '#' portions, another for '?' portions, and the last one for '/' portions. Anyway, I am glad that more people are questioning about bioinformatics related stuffs.
Cheers!