EnteriX

EnteriX provides visualization and analysis of bacterial genome alignments to support comparative genomics of enterobacteria.

Key Features:

• Enteric: Generates a graphical hypertext view of pairwise alignments between a reference genome and related sequences covering approximately 20 kilobases around a specified genomic position and highlights insertions, deletions, and rearrangements with color-coding.
• Menteric: Computes and displays nucleotide-level multiple alignments within a 1 kilobase region surrounding a specified address and annotates open reading frames (ORFs) and regulatory sites.
• Maj: Java-based viewer that integrates Enteric and Menteric outputs, provides a zoom-in visualization mechanism, and presents alignment information in two formats for multi-scale examination.
• Multi-genome comparisons: Supports comparisons among over 15 enterobacterial genomes anchored on four different reference genomes.
• User sequence inclusion: Permits incorporation of user-provided sequences into alignments.
• Annotation and conservation detection: Identifies conserved regions and potential regulatory elements to aid functional assignment inference.

Scientific Applications:

• Comparative genomics: Enables comparative analyses across enterobacterial species including Escherichia coli K-12, Klebsiella pneumoniae, Yersinia pestis, Vibrio cholerae, and Salmonella enterica serovars Typhimurium, Typhi, and Paratyphi A.
• Detection of large-scale events: Facilitates identification of insertions, deletions, and rearrangements in genomic regions.
• Variant discovery: Has been used to detect specific genomic variations such as partial deletions in rffH, a gene involved in enterobacterial common antigen biosynthesis.
• Nucleotide-level functional inference: Supports analysis of ORFs, conserved sequence blocks, and regulatory sites for functional assignment and regulatory pattern inference.
• Pathogenicity and phylogenetics: Supports examination of sequence conservation and divergence to inform studies of pathogenicity and phylogenetic relationships.
• Host–pathogen interaction studies: Assists investigation of genomic features relevant to host–pathogen interactions.

Methodology:

Generates graphical hypertext pairwise alignments over ~20 kilobase regions; computes and displays multiple sequence alignments over 1 kilobase regions with ORF and regulatory-site annotations; integrates views in a Java-based Maj viewer with zoom and two alignment formats; supports anchoring on four reference genomes and inclusion of user-provided sequences.