Bioinformatics applications for evolutionary and ecologically high throughput sequence analysis (completed)
The main goal of this project is to use bioinformatics to develop new bioinformatics applications as a research tool.
About the project
This project focuses particularly on solving some of the major obstacles in bioinformatics analyses of large and complex data in the field of ecological and evolutionary microbiology. The availability of high throughput sequencing technology at lower cost than previously will certainly cause dramatic increase in the number of genome sequences in near future. The explosion of genomic sequence information generated immediate reliance upon ultra high throughput analysis in bioinformatics field.
An increase in the amount of large-scale sequence data does not necessarily lead to an increase in biological knowledge until it is accompanied with new or improved tools for sequence analysis. The main objective of this project is to develop a user-friendly bioinformatics infrastructure for data mining of sequence databases and downloading aimed for ultra high throughput sequence analysis.
This infrastructure, which we call GeneGrabber, will form the basis for developing one major web-based service freely available to anyone. In addition, this infrastructure will form the basis for developing two smaller bioinformatics applications in the areas of biodiversity (PhyloSity) and phylogenomics (AIR). All the web-based applications will be made available on the Bioportal at University of Oslo, and it is a goal to contribute to improve research in MERG by applying these applications in ongoing research.
To develop bioinformatics tools and subsequent analysis of ever increasing sequences in the context of ecological and evolutionary microbiology. To apply these newly developed tools on computer clusters (Bioportal) for ultra high throughput analysis.
- GeneGrabber: a user-friendly bioinformatics infrastructure for data mining of sequence database and downloading aimed for ultra high throughput sequence analysis.
- AIR (Appender, Identifier, Remover): A web based phylogenomic application for efficient creation of multigene alignments and better assessment of evolutionary rates in sequence alignments.
- PhyloSity: A web-based pipeline for clustering and phylogenetic analysis of environmental sequences.