Bioinformatics and Comparative Genomics Lab

Brock University, St. Catharines, Ontario
What the facility does

Research on genetic diversity using combined computational and experimental techniques

Area(s) of Expertise

Using an integrated approach combining computational and experimental comparative and functional genomics technologies, the Bioinformatics and Comparative Genomics Lab is interested in studying the mechanisms of inter- and intra-species genetic diversity and their contribution to the diversity of biological traits.

Research Services

Genomics software available for: Analysis of methylation data, Analysis of cytogenetic data, Exon prediction, Identification of genes, Access to databases: Retrotransposon Insertion, Polymorphism, Hermansky-Pudlak Syndrome, Comparative Cellular and Molecular Biology of Longevity

Sectors of Application
  • Life sciences, pharmaceuticals and medical equipment

Equipment

Function

Bioinformatics computational infrastructure and software

 

Methylation peak processor

Web tool used to process the NimbleGen DNA methylation data. There are two goals in analyzing this kind of data: (1) to find common peaks among samples and (2) to find peaks unique to a group.

KaryoReader

Parses the karyotypic data and calculates the detailed chromosomal changes, aiming to facilitate systematic analysis of cytogenetic data at large scales, such as the data in the Mitelman Database of Chromosome Aberrations in Cancer, and to identify novel cytogenetic signatures associated with specific genetic diseases

Prot2Gene

Precise Exon prediction and mapping using protein sequences

Gene filter

There are three programs on the website: gene filter program, gene annotation program and common probe (gene) selection program.

 

The gene filter program is used to put some constraints on a set of gene-expression data, such as fold change and minimum expression value. Unlike with statistical methods, we did not compute significance most of the time.

 

The gene annotation program is used to help find the annotation information for a set of specific genes or probes. This program needs to be further expanded. Currently, only Affymetrix data are in the database.

 

The common probe (gene) selection program is used to find genes or probes that are shared by different samples and can show the sampler specific genes or probes.

 

aCGHViewer

 

Retrotransposon Insertion Polymorphism (dbRIP)

dbRIP is a database of human Retrotransposon Insertion Polymorphisms (RIPs) in which RIPs are highly integrated into the human genome annotation data provided by UCSC Genome Browser. The database contains all currently known Alu, L1 and SVA polymorphic insertion loci in the human genome.

 

Hermansky-Pudlak Syndrome Database

This database provides integrated, annotative and curative data distributed in a variety of public databases or predicted by bioinformatics tools for the recently cloned human and mouse HPS genes, as well as the genes responsible for HPS-related syndromes, such as Chediak-Higashi, Griscelli, Usher type 1B and Waardenburg.

 

Comparative Cellular and Molecular Biology of Longevity

This database contains a wide range of cellular and molecular trait data from vertebrate species that have been collected by comparative biologists with the goal of identifying traits that are highly correlated with longevity. Currently, the database holds about 1,000 records from almost 100 individual studies.