Ryan's Blog

A Greedy Algorithm for Aligning DNA Sequences

Posted in research by ryanlayer on October 8, 2009

JOURNAL OF COMPUTATIONAL BIOLOGY Volume 7, Numbers 1/2, 2000

Paper

Abstract

For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors
from other sources, a greedy algorithm can be much faster than traditional dynamic programming
approaches and yet produce an alignment that is guaranteed to be theoretically
optimal.We introduce a new greedy alignment algorithm with particularly good performance
and show that it computes the same alignment as does a certain dynamic programming algorithm,
while executing over 10 times faster on appropriate data. An implementation of
this algorithm is currently used in a program that assembles the UniGene database at the
National Center for Biotechnology Information.

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Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion.

Posted in research by ryanlayer on October 8, 2009

Nucleic Acids Res. 2009 Aug 26.

Paper

Abstract

Paired end mapping of chromosomal fragments has been used in human cells to identify numerous structural variations in chromosomes of individuals and of cancer cell lines; however, the molecular, biological and bioinformatics methods for this technology are still in development. Here, we present a parallel bioinformatics approach to analyze chromosomal paired-end tag (ChromPET) sequence data and demonstrate its application in identifying gene rearrangements in the model organism Saccharomyces cerevisiae. We detected several expected events, including a chromosomal rearrangement of the nonessential arm of chromosome V induced by selective pressure, rearrangements introduced during strain construction and gene conversion at the MAT locus. In addition, we discovered several unannotated Ty element insertions that are present in the reference yeast strain, but not in the reference genome sequence, suggesting a few revisions are necessary in the latter. These data demonstrate that application of the chromPET technique to a genetically tractable organism like yeast provides an easy screen for studying the mechanisms of chromosomal rearrangements during the propagation of a species.