Gilles VACHON wrote:
>> Hi all,
>> I am trying to make nice alignments of two protein sequences for the first t=
> ime.
> I realize we don't have a software to make boxes etc...
> Someone told me Pretty box is useful to do the job.
> Is it available ot is there a similar program to nicely align seuences?
Gilles, do you want to *align* the two sequences,or display an existing
alignment? If the former, PRETTYBOX, PRETTYPLOT, BOXSHADE, ALSCRIPT etc.
will not help, as they all display preexisting multiple alignments. You
need a program to compute the optimum alignment of the two sequences. I
use the GCG programs GAP or BESTFIT for this, I haven't used any non-GCG
programs.
If you just want to display, PRETTYPLOT and PRETTYBOX are part of the
EGCG package, I think. The others are available from various FTP sites,
look at recent messages in this group.
best of luck,
Michael D. Baron
michael.baron at bbsrc.ac.uk
