a scalable method for analysis and display of dna sequences一个可伸缩的dna序列的方法进行分析和显示.pdfVIP

A Scalable Method for Analysis and Display of DNA Sequences 1 2 1 Lawrence Sirovich *, Mark Y. Stoeckle , Yu Zhang 1 Laboratory of Applied Mathematics, Mount Sinai School of Medicine, New York, New York, United States of America, 2 Program for the Human Environment, The Rockefeller University, New York, New York, United States of America Abstract Background: Comparative DNA sequence analysis provides insight into evolution and helps construct a natural classification reflecting the Tree of Life. The growing numbers of organisms represented in DNA databases challenge tree- building techniques and the vertical hierarchical classification may obscure relationships among some groups. Approaches that can incorporate sequence data from large numbers of taxa and enable visualization of affinities across groups are desirable. Methodology/Principal Findings: Toward this end, we developed a procedure for extracting diagnostic patterns in the form of indicator vectors from DNA sequences of taxonomic groups. In the present instance the indicator vectors were derived from mitochondrial cytochrome c oxidase I (COI) sequences of those groups and further analyzed on this basis. In the first example, indicator vectors for birds, fish, and butterflies were constructed from a training set of COI sequences, then correlations with test sequences not used to construct the indicator vector were determined. In all cases, correlation with the indicator vector correctly assigned test sequences to their proper group. In the second example, this approach was explored at the species level within the bird grouping; this also gave correct assignment, suggesting the possibility of automated procedures