Color of percentage identity in Jalview

great ! One thing to bear in mind though is that colour by annotation shades slightly differently - since the percentage identity calculation is appled to each type of residue in each column, rather than across the whole column (so the sequences with the residue identical to the consensus is dark blue, and the next most frequent residue is shaded a lighter blue… through to white).

If you’d like to vote for a real customisable Percent Identity or BLOSUM shading model to be implemented in the future, then sign up at our feature/bug database and vote on this page:



On 13/02/2015 13:34, Israel Hanukoglu wrote:

Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, College of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | []( | []( 
The University of Dundee is registered Scottish charity: No.SC015096

Hi Jim,

The conserved regions detected as ‘motifs’ by the MEME algorithm are very useful features to visualise in a multiple sequence alignment when looking at local conservation in multi domain protein evolution.
MEME provides text output file file and an html output file. Would it be possible to incorporate this type of shading into Jalview, say by reading a MEME output file and using it to shade the relevant sequences and strings within the sequences for each motif?



Ricardo Gonzalez Mendez, PhD
University of Puerto Rico School of Medicine