I got an alignment of orthological promoter sequences of 13 eutherian mammals created in ENSEMBL.org. I have found some motifs that are relatively well conserved among tested mammals and proved their activity in reporter gene assay. Now I would like to present a plot or graph showing which part of human promoter is conserved among this 13 mammals. I would like to create such a graph for human promoter in which one axis will correspond to the sequence and the other one to the level of sequence conservancy in a particular fragment of this sequence or other type of plot clearly showing which motifs are well conserved. Can anyone suggest a good tool for performing such a task? My goal is to quantitatively or semi - quantitatively (relatively) present the difference between the conservancy of a conserved motif and surrounding sequences in the promoter.
You could use DnaSP (http://www.ub.edu/dnasp/) to produce a sliding window analysis of nucleotide diversity. This would produce a plot in which the x-axys represents the length of the sequence alignment, and the y-axys represents the nucleotide diversity. Nucleotide diversity would be a proxy of sequence conservation, with conserved regions showing very low variation. An example of such plot can be seen in the second figure of this article:
http://www.sciencedirect.com/science/article/pii/S0001706X12001830
Thank you - I will try that approach - I hope it will work for my alignment of non-coding highly dissimilar sequence with only some motifs conserved.
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