Question

Which of the following is not true regarding the BLOCKS?

(a) The BLOCKS server can extract a conserved, ungapped region from a MSA to produce a sequence block

(b) The server can also find blocks in a set of unaligned, input sequences and maintains a large database of blocks based on an analysis of proteins in the Prosite catalog

(c) Blocks are found by the Protomat program

(d) The program MOTIF doesn’t locate spaced patterns

I got this question during an online exam.

This key question is from Localized Alignments in Sequences topic in portion Multiple Sequence Alignment of Bioinformatics

Answer 1

Right answer is (d) The program MOTIF doesn’t locate spaced patterns

Easiest explanation: Blocks are found in two steps: First, the program MOTIF described on the previous page is used to locate spaced patterns. The second step takes the best and most consistent patterns found in step 1 and uses the program MOTOMAT to merge overlapping triplets and extend them, orders the resulting blocks, and chooses those that are in the largest subset of sequences.