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

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

blast
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updated by Lyco Lyco • written by Beeth • Beeth

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

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written by Neilfws Neilfws

2 answers

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.

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written by Anima Mundi Anima Mundi

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)

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written by Lyco Lyco

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