Congratulations to ECE Professor Ashfaq Khokhar for receiving a new NSF grant of $200,000 as PI for a project titled ""EAGER: High Performance Algorithms and Implementations for Genome Alignment" from 9/1/2012 to 8/31/2014, Award No. CCF-1216825.
ABSTRACT
Analysis of biological sequences, including multiple sequence alignment,
motif finding, and genome alignment, is a fundamental problem in
computational biology due to its critical significance in wide ranging
applications including haplotype reconstruction, sequence homology,
phylogenetic analysis, and prediction of evolutionary origins. Most of
the sequence analysis problem formulations (particularly those related
to alignment) are considered NP-hard. Existing solutions to the sequence
alignment problem (both sequential as well as parallel) are extremely
limited in their applicability and yield poor performance for large data
sets. Moreover most of these solutions have been designed for aligning
short length sequences. The genome alignment problem (very long
sequences) is significantly harder and very few solutions exist that are
capable of constructing genomes from short reads while taking
significant amount of execution time.
This project deals with the design and development of high performance
algorithms and implementations for aligning genomes using innovative
sampling and domain decomposition strategies. This approach has never
been pursued for genome alignment in the past. The proposed algorithms
are implemented on hybrid computing platforms consisting of multicore
clusters and GPU units.
The proposed research brings together tools and applications from
multiple disciplines such as bioinformatics, computational biology,
statistics, and high performance computing. Therefore the findings will
introduce new tools for biology and biomedical applications. It will
facilitate rapid reconstruction of genomes and mapping of short reads to
the corresponding haplotypes.
Topic revision: r1 - 2012-08-28 - 16:25:31 - Main.ronaldf