Question

If the data set is _______ then unless the motif has __________ amino acids in each column, the column frequencies in the motif may not be highly representative of all other occurrences of the motif.

(a) small, distinct

(b) small, almost identical

(c) large, almost identical

(d) large, distinct

This question was addressed to me in homework.

This intriguing question originated from Position topic in chapter Multiple Sequence Alignment of Bioinformatics

Answer 1

Correct answer is (b) small, almost identical

The explanation is: The number of sequences for producing the motif may be small, highly diverse, or complex, giving rise to a second level of consideration. If the data set is small, then unless the motif has almost identical amino acids in each column, the column frequencies in the motif may not be highly representative of all other occurrences of the motif. In such cases, it is desirable to improve the estimates of the amino acid frequencies by adding extra amino acid counts, called pseudocounts, to obtain a more reasonable distribution of amino acid frequencies in the column.