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The Expectation Maximization algorithm has been used to identify conserved domains in unaligned...

The Expectation Maximization algorithm has been used to identify conserved domains in unaligned proteins only.

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asked Sep 11, 2021 in Bioinformatics by nolan (111k points)

The Expectation Maximization algorithm has been used to identify conserved domains in unaligned proteins only.

(a) True

(b) False

The question was posed to me in semester exam.

This is a very interesting question from Statistical Methods for Aiding Alignment topic in chapter Multiple Sequence Alignment of Bioinformatics

bioinformatics
multiple sequence alignment
statistical methods for aiding alignment

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1 Answer

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answered Sep 13, 2021 by myra (687k points)
selected Sep 13, 2021 by nolan

Best answer

Right option is (b) False

The explanation: This algorithm has been used to identify both conserved domains in unaligned proteins and protein-binding sites in unaligned DNA sequences (Lawrence and Reilly 1990), including sites that may include gaps (Cardon and Stormo 1992). Given are a set of sequences that are expected to have a common sequence pattern and may not be easily recognizable by eye.

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In EM algorithm, as an example, suppose that there are 10 DNA sequences having very little similarity with each other, each about 100 nucleotides long and thought to contain a binding site near the middle 20 residues, based on biochemical and genetic evidence. the following steps would be used by the EM algorithm to find the most probable location of the binding sites in each of the ______ sequences.

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