This is just a quick note about a handy tool that I have found very useful to display possible motifs or promoter sequences from an alignment in a graphical manner. We are working on a suite of tutorials on motif identification, and one of the nice ways to display the data when you are finished with some of the more texty-output tools is to use WebLogo.
Of course, you can use it for other things. Yes, I did do my name with this once….and here is another silly one as a quick example:
The size of the letters is proportional to their frequency in a stretch of nucleotides or amino acids. For example, if you have 4 sequences and A appears in the same place in all four, your A will be huge–100%size. If your T is in half of the places, the letter will be 50% height. If two nucleotides appear at equal frequency, you will see both at the same height. And so on. It is a useful way to look at regions and quickly understand how conserved a spot is.
Of course, in the paper there is an actual equation to demonstrate the whole thing, and if you are mathematically inclined you can check that out. And there are plenty of configuration options on the interface so you can color code and label and output in various ways.
Crooks, G.E. (2004). WebLogo: A Sequence Logo Generator. Genome Research, 14(6), 1188-1190. DOI: 10.1101/gr.849004