The well-known Smith-Waterman (SW) algorithm is the most commonly used method for local sequence alignments. However, SW is very computationally demanding for large protein databases. There exist several implementations that take advantage of computing parallelization on many-cores, FPGAs or GPUs, in order to increase the alignment throughtput. In this paper, we have explored SW acceleration on...

*Department of Ecology and Evolutionary Biology, Brown University, Box G-W, 80 Waterman Street, Providence, Rhode Island 02912, USA; †Department of Biology, College of New Jersey, 2000 Pennington Road, Ewing, New Jersey 08628, USA; ‡Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, California 90095, USA; and §Department of E...

Jessie Dezutter, KU Leuven, Belgium Alan S. Waterman, The College of New Jersey, USA Seth J. Schwartz, University of Miami, USA Koen Luyckx, KU Leuven, Belgium Wim Beyers, Ghent University, Belgium Alan Meca, Florida International University, USA Su Yeong Kim, University of Texas, USA Susan Krauss Whitbourne, University of Massachusetts, USA Byron L. Zamboanga, Smith College, USA Richard M. Lee...

A polytope P of 3-space, which meets a given lattice L only in its vertices, is called L-elementary. An L-elementary tetrahedron has volume ≥ (1/6). det(L), in case equality holds it is called L-primitive. A result of Knudsen, Mumford and Waterman, tells us that any convex polytope P admits a linear simplicial subdivision into tetrahedra which are primitive with respect to the bigger lattice (1...

Error correction is the first step for any de novo assembly using next generation sequencing (NGS) data. This task is quite difficult and most available error correction software only supports base mismatches. In this work we propose a novel approach based on spectral graph clustering and Smith-Waterman alignment. This approach not only supports insertions and deletions, but also do not make an...

BRANDON J. GOFF, DO*; THANE D. McCANN, MD†; RUPAL M. MODY, MD‡; JOSHUA D. HARTZELL, MD; PAIGE E. WATERMAN, MD; LUIS J. MARTINEZ, MD¶; ROBERT N. WOOD-MORRIS, MD**; CHARLOTTE CARNEIRO, RN, MS, COHN-S, CIC††; RICHARD F. TROTTA, MD‡‡; JULIE A. AKE, MD, MSC; AENEAS JANZE, MD; ALLISON FRANKLIN, DO¶¶; SHANE McNAMEE, MD***; GARTH T. GREENWELL, DO†††; VINCENT T. CODISPOTI, MD‡‡‡; KEVIN F. FITZPATRICK, M...

The algorithm of Waterman et al. (1976) for malchirlg biological seyuences was modified under some limitations to be accomplished in essentially MN steps, instead of the M’lV steps necessary in the original algorithm. The limitations do not seriously reduce the generality of the original method, and the present method is available for most practical uses. The algorithm can be executed on a smal...