Biology Reference
In-Depth Information
Fig. 1 Comparing alternative alignments of the same sequence set with ALTAVIST at Bielefeld Bioinformaitcs
Server (BiBiServ). Two ways of using the program are offered. With OPTION 1, a set of nucleic acid or protein
sequences is uploaded. The server then runs DIALIGN and CLUSTAL W on the sequences and graphically
shows the positions in the two output alignments where these alignments agree. With OPTION 2, two pre-
calculated MSAs of the same sequence set can be entered and are compared in the same way
common practice to post-process MSAs manually. Various
alignment editors are available for this purpose, e.g., the widely
used program
JalView
[
39
].
One way to assess the (local) reliability of automatically calcu-
lated multiple alignments is to run different MSA programs on the
same set of input sequences and to compare the results. Generally,
those parts of the sequences that are aligned in the same way by
different MSA programs should be more reliable than regions that
are differently aligned. We developed a program called
ALTAVIST
(ALTernative Alignment VISualisation Tool)
that compares two
MSAs of the same sequence set and highlights those parts of the
MSAs where both programs agree [
40
].
At the bioinformatics server
BiBiServ
, this program can be
run in two different ways. (1) A sequence set can be entered,
and the MSA programs
CLUSTAL W
and
DIALIGN
are run on
these sequences. The program then highlights residues aligned in
