Question

Dayhoff, 1978- 1983, devised a second method for testing the relatedness of two protein sequences that can accommodate some local variation. Where this method is useful?

(a) For finding repeated regions within a sequence

(b) For finding similar regions that are in a different order in two sequences

(c) For finding small conserved region such as an active site

(d) For finding huge regions within sequences

I got this question by my college professor while I was bunking the class.

The origin of the question is Assessing the Significance of Sequence Alignments topic in chapter Sequence Alignment of Bioinformatics

Answer 1

Right answer is (d) For finding huge regions within sequences

Explanation: As used in a computer program called RELATE (Dayhoff 1978), all possible segments of a given length of one sequence are compared with all segments of the same length from another. An alignment score using a scoring matrix is obtained for each comparison to give a score distribution among all of the segments. A segment comparison score in standard deviation units is calculated as the difference between the values for real sequences minus the average value for random sequences divided by the standard deviation of the scores from the random sequences.