Talk:Sequence motif

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This article has comments here.

Brackets[edit]

In my browser, in plain text, square brackets show up as square brackets inside code tags([X]), while bolded square brackets show up as curly brackets ([X]). This means that bolding the bracket in the definition "This pattern may be written as N{P}[ST]{P} where N=Asn, P=Pro, S=Ser, T=Thr; {X} means any amino acid except X; and [XY] means either X or Y" makes things confusing.

It's also a little confusing that square brackets with one element means "not" while square brackets with more than one element means "or".

I am not a bioinformatics person, so I don't know if the brackets are supposed to be square or curly; I just know that it's confusing as is. Ducky 00:37, 14 October 2006 (UTC)

Arg. Never mind, the problem was with my font, not with the page contents. My mono unbolded curly brace showed up as a square bracket. I reverted. Ducky 00:46, 14 October 2006 (UTC)

Vaguely described[edit]

The topic is very vaguely described. It jumps from short sequences like the glycosylation motif to small domains covering 150 amino acids. Some of the stuff from the motif discovery section should be removed and placed into the linear motif entry. Other material should be moved to the entry on protein domains.

This topic should better encompass both DNA and protein sequence motifs without going into too much detail. doopa 08 Oct 2009

de novo searches vs. scans with known patterns[edit]

This article does not distinguish two fundamental types of sequence motif uses/algorithms. Sometimes one wishes to find, de novo, both an overrepresented pattern (e.g., as described by a position weight matrix) and its instances within a (DNA) database. At other times, one already knows the pattern and wants to scan for its instances within a (DNA) database. Shouldn't this distinction be described in the article? Shouldn't the software applications be divided into categories based upon which problem they solve? —Quantling (talk | contribs) 13:31, 29 April 2011 (UTC)