Menteric::Description

The Menteric web server computes and displays nucleotide-level multiple alignments of sequences from several related bacterial or viral genomes, together with annotations of functional sites and conserved regions. Views are calculated in a 1Kb region starting at the user-specified address in the reference genome, or centered about the start site of the user-supplied gene. The alignment is rendered as a PostScript or PDF document. A list of current reference genomes can be found here.

Locations of known functional sites are shown as color coded underlays on the alignment. Promoter regions are shown in green, protein binding sites in red, and genes (ORFs) 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. Annotation data for functional landmarks were collected from the GenBank page for each reference genome. In addition, conserved regions associated with potential functional sites are shown surrounded by boxes. The user can select from several types of conservation criteria for displays. 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. For instance, clicking on a gene's name leads to its entry in the Entrez Gene repository, and promoter and protein binding site labels are linked to the source of annotation data, where available. An abbreviation for the species name is indicated at the right end of each line. 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.