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» Dynamic programming alignment accuracy
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APPT
2007
Springer
13 years 9 months ago
A Parallel BSP Algorithm for Irregular Dynamic Programming
Dynamic programming is a widely applied algorithm design technique in many areas such as computational biology and scientific computing. Typical applications using this technique a...
Malcolm Yoke-Hean Low, Weiguo Liu, Bertil Schmidt
BMCBI
2007
136views more  BMCBI 2007»
13 years 7 months ago
Comparison of protein structures by growing neighborhood alignments
Background: Design of protein structure comparison algorithm is an important research issue, having far reaching implications. In this article, we describe a protein structure com...
Sourangshu Bhattacharya, Chiranjib Bhattacharyya, ...
CSB
2004
IEEE
123views Bioinformatics» more  CSB 2004»
13 years 11 months ago
A New Hardware Architecture for Genomic and Proteomic Sequence Alignment
We describe a novel hardware architecture for genomic and proteomic sequence alignment which achieves a speed-up of two to three orders of magnitude over Smith-Waterman dynamic pr...
Greg Knowles, Paul Gardner-Stephen
CC
2007
Springer
157views System Software» more  CC 2007»
14 years 1 months ago
New Algorithms for SIMD Alignment
Optimizing programs for modern multiprocessor or vector platforms is a major important challenge for compilers today. In this work, we focus on one challenging aspect: the SIMD ALI...
Liza Fireman, Erez Petrank, Ayal Zaks
QRE
2010
129views more  QRE 2010»
13 years 6 months ago
Improving quality of prediction in highly dynamic environments using approximate dynamic programming
In many applications, decision making under uncertainty often involves two steps- prediction of a certain quality parameter or indicator of the system under study and the subseque...
Rajesh Ganesan, Poornima Balakrishna, Lance Sherry