ALIGNMENT-FREE APPROACH IN GENOMIC SEQUENCE COMPARISON

University Of Nebraska Medical Center, Omaha NE

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Abstract

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The massive amount of data inundating life scientists is a common denominator driving various bioinformatics research activities. There are many interesting problems in life sciences whose solutions are hidden in these data and there are many potential approaches in the engineering and computer science domain to finding solutions to these problems. Dr. Bastola's research is focused on computational tool development and deployment in bioinformatics. Traditionally we have used single target genes (rRNA for ribosomal small or large subunits) for developing rapid identification assays and studying evolutionary mechanisms in living organisms. Computational tools like the BLAST developed for such studies employ alignment-based pair-wise sequence comparison. Today we have access to genomic sequences for a number of organisms, and biologically meaningful information can be obtained from comparative genomic analysis of the whole genome. Alignment-based computational tools cannot handle genome comparison and represent a serious limitation and hindrance to the discoveries that are possible with comparative genomic analysis. The proposed study will evaluate an alignment-free approach to genomic sequence comparison, where information content in the DNA is compared instead of the nucleotide sequence. This approach requires us to visualize both DNA encoding and computer programming to follow a simple linear progression from information to function: DNA to protein in biology, and High Level Language to executable machine instructions in computers