Question: Is A Gap At The Same Position In Query And Template Possible?
1
gravatar for Beeth
8.0 years ago by
Beeth170
Beeth170 wrote:

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 • 1.4k views
ADD COMMENTlink written 8.0 years ago by Beeth170

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

ADD REPLYlink written 8.0 years ago by Neilfws48k
6
gravatar for Anima Mundi
8.0 years ago by
Anima Mundi2.4k
Italy
Anima Mundi2.4k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Anima Mundi2.4k
3
gravatar for Lyco
8.0 years ago by
Lyco2.3k
Germany
Lyco2.3k wrote:

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)

ADD COMMENTlink written 8.0 years ago by Lyco2.3k
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