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BMCBI
2010
153views more  BMCBI 2010»
15 years 11 days ago
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massi
Background: Massively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation. Pash 3.0 performs sequen...
Cristian Coarfa, Fuli Yu, Christopher A. Miller, Z...
117
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IPPS
2005
IEEE
15 years 6 months ago
High-Performance Direct Pairwise Comparison of Large Genomic Sequences
Many applications in Comparative Genomics lend themselves to implementations that take advantage of common high-performance features in modern microprocessors. However, the common...
Christopher Mueller, Mehmet M. Dalkilic, Andrew Lu...
101
Voted
BMCBI
2010
90views more  BMCBI 2010»
15 years 27 days ago
Local alignment of generalized k-base encoded DNA sequence
Background: DNA sequence comparison is a well-studied problem, in which two DNA sequences are compared using a weighted edit distance. Recent DNA sequencing technologies however o...
Nils Homer, Stanley F. Nelson, Barry Merriman
BMCBI
2004
150views more  BMCBI 2004»
15 years 19 days ago
SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters
Background: Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a u...
Chunlin Wang, Elliot J. Lefkowitz
AINA
2006
IEEE
15 years 6 months ago
Accelerating the HMMER Sequence Analysis Suite Using Conventional Processors
Due to the ever-increasing size of sequence databases it has become clear that faster techniques must be employed to effectively perform biological sequence analysis in a reasonab...
John Paul Walters, Bashar Qudah, Vipin Chaudhary