What are DNA sequence motifs? Why are they important?
DNA sequence motifs are used to profile a genomic region in DNA. They are characterized as short nucleotide patterns and are conserved at biologically related genomes. The complexity of these patterns ranges from a simple and short subsequence (5-20 bp long) to palindromic and space dyed subsequences. In essence, motifs are considered as a means of enciphering DNA and are key element for defining regulatory networks and further understand the interactions between transcription factors and DNA .
How are motifs formulated?
There are several models that could be used to represent a sequence motif, including but not limited to consensus ...view middle of the document...
Also, many solutions and technologies have been developed to address each of the problems. Following is a broad breakdown of motif analysis to clearly understand and envision how it is performed:-
I, Preprocessing stage
At this stage we wish to construct a set of co-regulated genes, presuming that they share a biologically function. This is typically addressed by experimentation .e.g. observing protein interaction with DNA at small-scale genomic regions. It is shown that such experiments are efficient and yield reliable results, especially when applied on simple genomic sequences. But, their performance degrades as the genomic complexity of the cell increases. To overcome this issue, phylogenetic footprinting (cross-species genomic analysis) is used .
Having obtained the set of putative genomes (from I), we would like to extract the signals that occur at all sequences (the motifs). This is a challenging task, because it depends on various factors, such as the quality of the sequences, and it has some unknown parameters, like the size and orientation of the motifs. There are two main methods used to address this problem:- ...