HW3 1b

[Orion]

Regarding gapped motifs, we would appreciate a little clarification:

What does it mean to have a gapped motif of length K? Are there K non-
gap characters, where gaps can be found between any pairs without
penalty? Or is the total length of the motif K, where some of those
characters are gaps?

In the assignment description, it says to treat gaps as a 5th DNA
character "for simplicity." This would imply that in a local
alignment, we should treat inserting a gap as the same as a mismatch.

For instance, given a local alignment:
ATTTTG
ACCCCG

The following two "left-out" sequences would score the same?
AG
AAAAAG

Danke,
Orion

[Michael Brudno]

The second: the total length is K, and some characters can be gaps.

[Orion Buske]

Okay, and to clarify with an example, given a local alignment:
ATTTTG
ACCCCG

The following two "left-out" sequences would score the same because gaps are just another character?
AG
AAAAAG

Sorry for the persistence; just trying to make sure I understand,
Orion

[Michael Brudno]

yes.