- Traditional methods obtain a microorganism's DNA by culturing it individually. Recent advances in genomics have lead to the procurement of DNA of more than one organism from its natural habitat. Assembling these genomes is a crucial step irrespective of the method of obtaining the DNA.
- The goal of this project is to develop a fuzzy method for multiple genome sequence assembly of cultured genomes (single organism) and environmental genomes (multiple organisms). Our proposed solution is a sequence assembly based on fuzzy logic, which allows for tolerance of inexactness or errors in fragment matching and that can be used for improved assembly. The method uses fuzzy classification using modified fuzzy weighted averages to classify fragments belonging to different organisms within an environmental genome population. The approach uses DNA-based signatures such as GC content and nucleotide frequencies as features for the classification.
- Adrienne Breland, Karen Schlauch, Monica Nicolescu, and Frederick Harris, "An Annotated k-deep Prefix Tree for (1-k)-mer Based Sequence Comparisons", in the "ACM International Conference on Bioinformatics and Computational Biology", August 2-4, New York, USA, 2010. [PDF] [LINK]
- Sara Nasser, Adrienne Breland, Frederick C. Harris Jr., Monica Nicolescu, and Gregory L. Vert, "Fuzzy Genome Sequence Assembly for Single and Environmental Genomes", in Fuzzy Systems in Bioinformatics, Bioengineering and Computational Biology, Springer Book Series on Studies in Computational Intelligence, 2009. [PDF]
- Sara Nasser, Adrienne Breland, Frederick Harris Jr, Monica Nicolescu, "A Fuzzy Classifier to Taxonomically Group DNA Fragments within a Metagenome", in Proceedings of the North American Fuzzy Information Processing Society Conference, New York, NY, May, 2008. [PDF]
- Sara Nasser, Gregory Vert, Monica Nicolescu, Alison Murray "Multi Sequence Assembly for Prokaryotes and Eukaryotes Using Fuzzy Logic", IEEE International Journal of Information Technology and Intelligent Computing, vol. 2, no. 4, 2007. [PDF]
- Sara Nasser, Gregory Vert, Monica Nicolescu, "Fuzzy Classification of Genome Sequences Prior to Assembly Based on Similarity Measures", in Proceedings, the North American Fuzzy Information Processing Society Conference San Diego, CA, June 24-27, 2007. [PDF]
- Sara Nasser, Gregory Vert, Monica Nicolescu, "Multiple Sequence Alignment using Fuzzy Logic", in Proceedings, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, Honolulu, HI, April 1-5, 2007. [PDF]
- This work was supported by the National Science Foundation EPSCoR Ring True III award EPS0447416.