My understanding is that alignments reported by ncbi blast* tools are always listed in order of decreasing score. However after setting up blastp with a local database I am seeing output where this is not the case as shown below. As evident, the alignment scores are not in listed decreasing order. Any thoughts on what might cause this? thanks. ---
Sequences producing significant alignments: (Bits) Value HLA:HLA00355 B*51:10 232 bp 471 0.0 HLA:HLA03555 G*01:04:05 273 bp 469 0.0 HLA:HLA00950 G*01:04:02 273 bp 469 0.0 HLA:HLA03552 G*01:01:16 273 bp 470 0.0 HLA:HLA03553 G*01:01:15 273 bp 470 0.0 HLA:HLA00945 G*01:01:07 273 bp 470 0.0 HLA:HLA03159 G*01:01:14 273 bp 470 0.0 HLA:HLA03558 G*01:01:19 273 bp 470 0.0 HLA:HLA03556 G*01:01:17 273 bp 470 0.0 HLA:HLA03557 G*01:01:18 273 bp 470 0.0 HLA:HLA13776 G*01:19 273 bp 468 0.0 HLA:HLA03396 G*01:12 273 bp 468 0.0 HLA:HLA01802 A*02:67 270 bp 471 0.0
•
written
by
willing_mh •
3 answers
BLAST always reports hits in order of decreasing max_score of found HSPs (E-value is also calculated based on maximal score of HSP).
What you see in your output is total_score for a hit. Total score is a sum of HSPs' scores for a given hit. I can only see a fragment of your BLAST output, but I bet that BLAST found one HSP for your top-ranked sequence HLA:HLA00355. It means it is aligned to your query in one segment which achieved the highest score (471 bits). In this case total_score equals max_score. However, the sequence from the botttom of your output (HLA:HLA01802) achieved the same total_score (471 bits), but its alignment is splitted into more than 1 HSP. For example, one HSP could have score of 400 and the other one is 71, they both sum to total score of 471.
Scroll down your results and look at the alignments to see these differences between scores for HLA:HLA00355 and HLA:HLA01802.
•
written
by
Andrzej Zielezinski
As far as I remember, the default sort order is based on e-value.
•
written
by
Jean-Karim Heriche
Log in to answer this question.
thanks for your comment - I reformatted the blastp output so it is easier to read: the e-value is reported at 0.0 for all entries but the score both decreases and increases
Because blastp sorts by e-value, equal e-values are output in random order.