EnteriX 2003 -- Visualization tools for genome alignments of Enterobacteriaceae
What you can do:
Use a suite of three web-based visualization tools to graphically display alignment information from comparisons among several fixed and user-supplied sequences from related enterobacterial species, anchored on a reference genome.
Highlights:
- The first visualization, Enteric, displays stacked pairwise alignments between a reference genome and each of the related bacteria, represented schematically as PIPs (Percent Identity Plots). Encoded in the views are large-scale genomic rearrangement events and functional landmarks.
- The second visualization, Menteric, computes and displays 1 Kb views of nucleotide-level multiple alignments of the sequences, together with annotations of genes, regulatory sites and conserved regions.
- The third, a Java-based tool named Maj, displays alignment information in two formats, corresponding roughly to the Enteric and Menteric views, and adds zoom-in capabilities.
- The uses of such tools are diverse, from examining the multiple sequence alignment to infer conserved sites with potential regulatory roles, to scrutinizing the commonalities and differences between the genomes for pathogenicity or phylogenetic studies.
- The EnteriX suite currently includes >15 enterobacterial genomes, generates views centered on four different anchor genomes and provides support for including user sequences in the alignments.
Keywords:
- enterobacterial genomes
- enterobacteria comparative genomics tool
- transcription factor binding site prediction tool
- cis-elements prediction tool
- cis-regulatory elements prediction tool
- promoter analysis tool
- promoter elements prediction tool
- sequence alignment tool
- multiple sequence alignment tool
- DNA sequence alignment tool
- comparative genomics tool
- genomic sequence alignment tool
- gene prediction tool
- DNA sequence analysis tool
- genomic sequence analysis tool
- genome alignment tool
- whole-genome alignment tool
- Escherichia coli genome
- E. coli genome
- bacterial genomes
- Salmonella genomes
Literature & Tutorials:
This record last updated: 06-14-2005