error reporting gaps in blastx output

sequenceserver
#1

Hi there, Sequenceserver is really helping me out in my research. I just noticed one issue: in alignments that clearly have gaps, gaps are always reported as 0. I’ve noticed this in blastx results

Here’s an example that has many gap positions, but reported as 0/46

Hit length: 135 Select | Sequence | FASTA
1.
Score E value Identities Gaps Query frame
26.95 (58) 9.29 16/46 (34.78) 0/46 (0.00) -3

Query 636 PVRLGHHILRRVVAADFPKLPHPTLKHRRVPQLLPLQPILRHIPEK 499
P+ L H RRV A FP + +R P+++P +RH EK
Subject 59 PIGLTHFFTRRVPAHTFPGMHTCPGLSQRGPKIVPWVKEIRHTNEK 104

I’m using v1.0.8 with blast 2.2.30+

#2

In the example you gave what I think you are calling a gap is actually a mismatch. Below is an example of gap: the portion “EVT————————TLD” in the Subject line.

Score E value Identities Gaps Query frame

24.25 (51) 7.57 × 10-01 13/53 (24.53) 8/53 (15.09) 1
Query 160 RLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNN 318 RL R N +Y P K +A ++ +D+ + ++ E CP+N Subject 5 RLEVASRVNEAYGSPXSKFKFKAAEVT--------TLDEDIKVRVEEVCPINR 49

Gap is when you shift the sequences left/right to generate a more significant alignment.

Priyam

#3

Oh, yes, you are totally right, So sorry for wasting your time!
Thanks for the note!
Best wishes
Simon