Attention: if you use Adobe Acrobat to view these PDF files, be sure to
read these
instructions!
A one page bird's eye view of the genome-wide pairwise alignments of E. coli K-12 with the other genomes is available in a single very large (12MB) PDF file.
Similarly, a genome-wide view of the pairwise alignments of
S. typhimurium LT2 with the other genomes is
here.
The Enteric server produces a graphical, hypertext view of the
pairwise alignments of the selected reference genome
(i.e., E. coli K-12, E. coli O157:H7,
S. typhimurium LT2, S. typhi CT18 or S. paratyphi A) with several related
bacteria
covering 20Kb around a user-specified position or gene in the reference organism.
Other organisms can be integrated as sequence data become available.
For each of the compared bacteria, all significant pairwise alignments with
the reference sequence in the selected region were computed with a locally
developed DNA sequence alignment tool called blastz. The
alignment information is displayed as a set of ``PIPs'' (Percent Identity
Plots), in which positions in the reference sequence are shown
along the horizontal axis and each match between the reference sequence
and the other bacterial sequence is represented as a
horizontal line. The percent identity of each match, a value between
50% and 100%, is then indicated by its vertical coordinate.
Additional information is embedded in each PIP. For instance,
in the E. coli K-12 and O157:H7 comparative views, clicking
on E. coli gene names (shown at the top of the PIP) links to their
Entrez Gene classifications.
Pointing at an alignment reveals the name of the contig matching that
E. coli region. Colored vertical stripes at the ends of some
alignments indicate the reason why that alignment terminated in the
other species. Red marks sequences in
the other species whose immediate neighbor has a homolog elsewhere in
E. coli, and pointing at the stripe displays that other E.
coli address. Blue marks sequences in
the other species whose immediate neighbor has no detectable homolog in
E. coli, and pointing at the stripe displays
the length of the unmatched sequence. The other colored regions have
no associated messages; for instance, yellow
is used for regions of the reference sequence not found in the
other species. Regions apparently not sequenced in the
other species are marked with gray.
NOTE: the significance of the color bar features for alignments
in the user sequence is somewhat different. Since the sequence provided
was aligned only with the 20Kb query region, and not with the entire
reference genome, for performance reasons, the annotations should be interpreted
with respect to that range.