Question

Which of the following is untrue regarding the block analysis method?

(a) Blocks represent a conserved region in the MSA

(b) Blocks differ from profiles in lacking insert and delete positions in the sequences

(c) Every column includes only matches and mismatches

(d) Blocks may be made by searching for a section of an MSA alignment that is low conserved

This question was posed to me during a job interview.

I need to ask this question from Localized Alignments in Sequences in portion Multiple Sequence Alignment of Bioinformatics

Answer 1

Correct answer is (d) Blocks may be made by searching for a section of an MSA alignment that is low conserved

The best explanation: Like profiles, blocks may be made by searching for a section of an MSA alignment that is highly conserved. However, aligned regions may also be found by searching each sequence in turn for similar patterns of the same length. These patterns may include a region with one or a few matching characters followed by a short spacer region of unmatched characters and then by another set of a few matching characters, and so on, until the sequences start to be different.