Genome Analysis Tools module

Genome comparison and analysis

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

Chromosome comparison window

16S metagenomics

The Genome Analysis Tools module provides metagenomics tools for characterizing microbial communities based on deep sequencing of a taxonomical marker gene.

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

Features:

Comparative genomics tools

BioNumerics lets you align and compare sequences of up to full chromosome length. Discontinuous alignments are calculated using seed and stretch-based sequence mapping, revealing genomic inversions, swaps, duplications, insertions and deletions. Mutation and SNP discovery can be performed on template-based multiple chromosome alignments, with optional selection of mutation type (intergenic, synonymous, non-synonymous or indel) and filtering of significant SNPs based on quality scores. dNdS analysis based on the ratio synonymous/non-synonymous mutations within gene clusters is available to predict evolutionary selection pressure on genes.

Deep sequencing of microbial communities

BioNumerics provides comprehensive metagenomics tools for the characterization of microbial communities using deep sequencing of a phylogenetic marker (e.g. 16S rRNA). Operational Taxonomic Unit (OTU) quantification, visualization and comparison of microbial communities starting from the raw sequence reads now becomes feasible!

Genome annotation

Unannotated or partially annotated sequences can be annotated against one or multiple reference chromosomes. For each annotated ORF, all possible choices are listed according to feature identity and chromosome synteny. Similar features can be clustered according to identity. The user can manually override annotations made by the software.