Enteric::Description

The Enteric server produces a hypertext view of the pairwise alignments of a reference genome with several related bacterial or viral genomes covering 20Kb around a user-specified position or gene in the reference. A list of currently supported reference genomes is here. Other organisms can be integrated upon request, and as sequence data become available.

For each of the compared genomes, pairwise alignments with the reference sequence in the selected region were computed with the DNA sequence alignment tool 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, clicking on the genes names at the top of the (say) E. coli PIPs 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.
• Yellow is used for regions of the reference sequence not found in the other species.
• Gray marks regions apparently not sequenced in the other species.

Enteric allows one user specified sequence (USR) to be included in the comparative views in a reference genome region of interest. However, please note that the significance of the color bar features for alignments in the user sequence is somewhat different. Since the sequence provided is aligned only with the 20Kb query region, and not with the entire reference genome, the annotations must be interpreted with respect to that range.