Bioinformatics Solutions (Canada)
Publishes on Topological and Geometric Data Analysis, Genomics and Phylogenetic Studies, Geometric and Algebraic Topology. 4 papers and 498 citations.
Add your photo, update your bio, and get notified when your ranking changes.
Extending the single optimized spaced seed of PatternHunter to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search technology back to a full circle.
Extending the single optimized spaced seed of PatternHunter(20) to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search methodology research back to a full circle.
UNLABELLED: New ideas, spaced seeds and gapped alignment before 6-frame translation are implemented for translated homology search in tPatternHunter. The new software compares favorably with tBLASTx. AVAILABILITY: The software is free to academics at http://www.bioinformaticssolutions.com/downloads/ph-academic/ CONTACT: bma@csd.uwo.ca.
A problem in a recent competition was: Given a 2004 by 2004 square grid of dots, what is the largest number of edges of a convex polygon whose vertices are dots in the grid? Of course, the question can be asked for any value of 2004, say n. For n = 2, 3 and 4 it’s easy to see (Figure 1) that the answers are p = 2n: 4 6 8 Figure 1: The best polygons for n = 2, 3 and 4 The next three (Figure 2) are not quite so obvious: