#DOTD: Sequence Motifs

19 Jul 2017

Sequence motifs are conserved sub-sequences which have structural or functional significance. In DNA, they could be promoters/terminators, enhancers/silencers, transcription factor/enzyme recognition sites. In RNA, they could be riboswitches, and in proteins, these could be nucleotide-binding domains.

 

Sequence motifs come in three different flavours:

1. Palindromic motifs

These types of motifs are also palindromes. An example of this is 5'-GCATATGC-3' because 5'-ATGC-3' is the reverse complement of 5'-GCAT-3'.

2. Gapped motifs

Also known as spaced or dyad motifs, these exist in two parts, with a fixed-length non-conserved gap in between. 

3. Degenerate motifs

These take into account SNPs. For example, 5'-TTATMCAMA-3' is a DnaA box which occurs near + within the origin of replication in E. coli. The fifth position is known as degenerate because M = C or A. Note that degenerate motifs can also be gapped or palindromic, or both!

4. Regular motifs

The remainder of motifs fall in to this category.

 

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Some parts of this post are based on the following paper:

Das, M.K. and Dai, H.K., 2007. A survey of DNA motif finding algorithms. BMC bioinformatics, 8(7), p.S21.

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PhDomics by Fatima