The Chromosome Comparison and Alignment module

BioNumerics uses proven technology acquired from the Kodon software to bring various specialized chromosome comparison and analysis functions. The Chromosome Comparison module offers side-by-side comparison of genomes and chromosomes, analysis of organization and functional behavior of genomes, alignment of multiple chromosomes and chromosome-based SNP analysis.

NxN pairwise chromosome comparison

• Extremely fast pairwise matching and alignment of NxN sequences of full chromosome size.
• Seed and stretch based sequence matching, allowing for discontinuous alignments, including inversions, swaps, duplications, insertions and deletions.
• Full-sequence based or coding sequence based alignment, using user-defined nucleic acid seeds and/or amino acid seeds.
• Display of clickable NxN chromosome similarity matrix and associated clustering. The selected pair of chromosomes is displayed in the dot plot Cell panel. Direct and inverted matches are displayed in different color.
• Clickable dot plot matrix, updating (1) currently selected stretch in the Stretches panel and (2) associated alignment in the Pairwise alignment panel.
• Calculation of superstreches, i.e. larger clusters of stretches that contain no major discontinuities and that have a minimal overall homology.

Template-based multiple chromosome alignment

• Alignment of multiple chromosomes based upon selected template chromosome.
• Display of overview panel and detailed multiple alignment panel.
• Synchronized selection in overview, multiple alignment, dot plot, stretches and pairwise alignment panels.
• Versatile search and display functions for features and subsequences on multiple chromosomes.

Mutation and SNP analysis

• Search and display of mutations within multiple alignments, with discrimination between intergenic, synonymous, non-synonymous and Indel mutations.
• Additional filtering based on SNP quality scores.
• Display colors based on mutation type or quality; sorting based on position, gene, NA change, AA change, quality (see figure above, Mutation analysis panel).
• Direct clustering based upon mutations or export of mutation list for further analysis.

dNdS ratio analysis

The dNdS ratio for a gene compares the non-synonymous mutations versus the synonymous mutations and as such, provides information on the positive selection pressure of the gene. The starting point in BioNumerics is a template-based multiple chromosome alignment. For each ORF on the template sequence, the aligned ORFs on the other sequences (if any) are grouped and synonymous/non-synonymous mutations are calculated for each codon. A list of dNdS ratios and related parameters for all ORFs is calculated, and the dNdS ratios can optionally be plotted in differential color on the multiple alignment.

Features:

• Pairwise multi-chromosome comparison. NxN pairwise comparison of sequences up to full chromosome length. Possibility to define, store and use multiple seeds for nucleic acid and amino acid based matching. Discontinuous alignments including inversions, swaps, duplications, insertions and deletions. Display of (clustered) NxN chromosome similarity matrix (Matrix panel) and dot plot for selected chromosome pair (Cell panel). Stretches and their properties are displayed in the Stretches panel and detailed pairwise alignment in the Pairwise alignment panel. All panels synchronize with one another by simple mouse clicks. Calculation of superstreches, i.e. larger clusters of stretches that contain no major discontinuities and that have a minimal overall homology. Possibility to add/remove chromosomes to alignment (program only recalculates new pairwise comparisons). 
• Multi-chromosome alignments. Multiple alignment of chromosomes based upon selected template chromosome. Possibility to calculate and store several multiple alignments based upon different template sequences. Synchronized selection in all panels (overview, multiple alignment, dot plot, stretches and pairwise alignment). Search and display functions for features and subsequences. dNdS analysis based on ratio synonymous/nonsynonymous mutations within gene clusters to predict evolutionary selection pressure on genes.
• Mutation and SNP analysis. Analysis of mutations within multiple alignments with optional selection of intergenic, synonymous, non-synonymous and indel mutations. Filtering of significant SNPs based on quality scores. Mutations are mapped on the multiple alignment and in a mutation list. Several colored display options based on mutation type or quality. Possibility to sort mutations on quality, position, type, gene, AA or NA change, etc. Clustering of sequences based upon mutations or export of mutation list for further analysis.

This module can only be used in combination with the Sequence Types Module.