This produces a 1000bp long alignment starting at a given location.
Color coding for alignment underlays:
| Light Chocolate -- Genes (ORFs); | Green -- Promoters; | Red -- Protein Binding Sites. |
The Menteric web server computes and displays nucleotide-level
multiple alignments of sequences from several related genomes in a 1Kb
region starting at the user-specified address, or centered about the
start site of the user-supplied gene. The alignment is rendered
as a PostScript or PDF document in which annotations of ORFs,
promoters and protein binding sites in the reference (i.e.,
E. coli K-12, E. coli O157:H7, S. typhimurium LT2,
S. typhi CT18 or S. paratyphi A) genome are color-coded.
Conserved regions, potentially associated with functional
sites, are surrounded by boxes.
Regulatory site annotations for E. coli K-12 were extracted
from the GenBank annotation version M54
(Blattner et al, 1997),
while gene information for E. coli K-12, E. coli O157:H7,
S. typhimurium LT2 and S. typhi CT18 was parsed from the gene tables
in the Entrez Genomes section. A list of S. paratyphi A genes was obtained from the
Genome Sequencing Center at the Washington University, St. Louis (WUSTL).
In addition to functional landmarks, the user can select from several
types of conservation criteria for identifying conserved regions to be
displayed. By default, regions longer than 6 nucleotides in which all
columns have a letter agreement better than 80% are reported as conserved.
When the output is displayed as a PDF document, the annotation labels
contain embedded links to various data repositories available on the
web. In the comparative views, clicking on a gene's name leads to its entry in the
Entrez Gene
repository, and promoter and protein
binding site labels are links to the source of annotation data, where available.
Clicking on the sequence name on the right-hand side of the
alignment downloads a web page containing the contig's sequence data
in the alignment range.
In the display, promoter regions are shown in green, protein binding sites in red, and genes (ORF's) in light chocolate. The label ``PR'' above a
green promoter band specifies that no experimental evidence has yet
been found for it (hence, it is a predicted promoter), and
``+1'' marks the start of transcription. An abbreviation for the species
name is indicated at the right end of each line.
List of abbreviations.