Talk:Multiple sequence alignment

some clarifications
the statement

Because HMMs are probabilistic, they do not produce the same solution every time they are run on the same dataset; thus they cannot be guaranteed to converge to an optimal alignment. HMMs can produce both global and local alignments. Although HMM-based methods have been developed relatively recently, they offer significant improvements in computational speed, especially for sequences that contain overlapping regions.

is incorrect. HMMs are probablistic in the sense that they are a statistical model, however, they are completely deterministic and will produce the same result every time on a given dataset. HMM alignments use the same algorithms as local sequence alignments and therefore have no computational speed advantage.

One of the most common motif-finding tools, known as MEME, uses expectation maximization and hidden Markov methods to generate motifs that are then used as search tools by its companion MAST in the combined suite MEME/MAST.[19][20]

MEME uses a PSSM (position specific scoring matrix), but does not contain insertion or deletion probabilities or other characteristics of a typical sequence HMM.

Gribskov 03:55, 20 September 2007 (UTC)

Short-read sequence alignment
Given the specific technological and algorithmic and biological significance of short-read sequence alignment, I think this topic deserves its own page. For example, the differences between short read mapping and de-novo assembly in next-generation sequencing projects could be discussed on such a page. --Dan|(talk) 14:01, 22 January 2009 (UTC)

Alternative interpretations of MSAs
The main use/interpretation of columns in MSAs is that residues in the same column are "related" by either point substitutions or no substitutions at all.

However, there are applications of MSAs where residues in the same column are assumed to be "structurally" equivalent but not necessarily evolutionarily equivalent e.g. http://www.ncbi.nlm.nih.gov/pubmed/16733545 - indeed in some of these applications the aim is to avoid including "homologous" sequences in the alignment e.g. http://www.ncbi.nlm.nih.gov/pubmed/9920390

At the moment this distinction isn't made on the MSA wikipedia page - although the top of the sequence alignment wikipedia page does highlight different interpretations.

First wikipedia post ever here - not quite ready to be bold yet! - so wanted to ask/check whether anyone disagrees with introducing some changes to reflect this distinction to the MSA page? SiggyDood (talk) 12:45, 11 March 2009 (UTC)

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