I am looking for a program which will allow me to display/print the
alignment I have made of a set of protein sequences. Ideally, it will
shade, or otherwise highlight, the residues that match a consensus,
allowing for conservative replacements; it would be nice to
distinguish highly conserved from less conserved residues.
I HAVE ALREADY TRIED the GCG program Prettybox, but found that there
are still some bugs in it, in that it makes some pretty strange
decisions as to what is the consensus, and doesn't respond properly to
the PLURALITY setting (which *should* allow one to say that one wants
at least X residues to agree before there is a consensus).This is sad,
as the program would otherwise seem to be perfect. I have also tried
BOXSHADE (ftp'd from the EMBL archive), which is also very nice, but
which insists on there being a consensus residue at every site, which makes
for a confusing picture.
I have tried PrettyPlot which works, but does not allow one to
distinguish between degrees of conservation (residues are either in
the box or out), and the PrettyPrint option in Don Gilbert's wonderful
SeqApp, which only highlights identical residues.
If you know of, or even have written, a program which displays
alignments, I would be grateful to hear from you. No commercial
software, I'm afraid, as there is no spare cash to buy anything at the
Thanks in advance,
Michael Baron (BARON at AVRI.AFRC.AC.UK)