Is A Gap At The Same Position In Query And Template Possible?

Question

[Beeth]

Hi:

I was wondering if a gap at the same position in query and template sequence is possible. Is that from a biological point of view possible or not?

As example:

ACTCC--CT
ACTCCC--G

Thanks Beeth

[Neilfws]

Have you observed this in the output from BLAST or other alignment software?

Answer 1

[Anima Mundi]

As the concept of gap itself derives from comparison (one sequence is gapped in respect to another), I would say that in a pairwise alignment a gap will never occur in both sequences. In a MSA two sequences could be gapped in respect to a third one, but in this case you would not have a conceptual separation between query and subjects.

Answer 2

[Lyco]

Generally, gaps like

ACTCC--CT
ACTCCC--G

don't have a biological meaning and are never reported by alignment programs (unless the result is a subset of a multi-species alignment) (or the program is broken)

More interesting are cases like this

ACTCC-GTAGTT
ACTCCC-TAGTT

which can be biologically meaningful although most alignment programs to not support them (transition from deletion-to-insertion state in HMM-speak)