Accelerating pairwise statistical significance estimation for local alignment by harvesting GPU's power.

PubWeight™: 0.75‹?›

🔗 View Article (PMC 3318904)

Published in BMC Bioinformatics on April 12, 2012

Authors

Yuhong Zhang1, Sanchit Misra, Ankit Agrawal, Md Mostofa Ali Patwary, Wei-Keng Liao, Zhiguang Qin, Alok Choudhary

Author Affiliations

1: School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China. yuhongzhang@uestc.edu.cn

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A (1988) 193.60

Identification of common molecular subsequences. J Mol Biol (1981) 130.53

BLAST+: architecture and applications. BMC Bioinformatics (2009) 36.53

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A (1990) 24.42

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99

Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol (2000) 12.05

Empirical statistical estimates for sequence similarity searches. J Mol Biol (1998) 4.14

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors. Bioinformatics (2000) 3.80

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics (2008) 3.71

Sensitivity and selectivity in protein structure comparison. Protein Sci (2004) 3.69

CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics (2011) 3.64

The estimation of statistical parameters for local alignment score distributions. Nucleic Acids Res (2001) 3.61

Accurate formula for P-values of gapped local sequence and profile alignments. J Mol Biol (2000) 3.51

Rapid and accurate estimates of statistical significance for sequence data base searches. Proc Natl Acad Sci U S A (1994) 2.72

The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions. Bioinformatics (2004) 2.08

CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Res Notes (2009) 1.96

Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches. Nucleic Acids Res (2006) 1.81

Making sense of score statistics for sequence alignments. Brief Bioinform (2001) 1.67

Computational biology. Bioinformatics--trying to swim in a sea of data. Science (2001) 1.64

CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions. BMC Res Notes (2010) 1.60

Statistical significance in biological sequence analysis. Brief Bioinform (2006) 1.46

Rapid assessment of extremal statistics for gapped local alignment. Proc Int Conf Intell Syst Mol Biol (1999) 1.20

Pairwise statistical significance of local sequence alignment using sequence-specific and position-specific substitution matrices. IEEE/ACM Trans Comput Biol Bioinform (2010) 0.89

Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments. BMC Bioinformatics (2010) 0.88

Island method for estimating the statistical significance of profile-profile alignment scores. BMC Bioinformatics (2009) 0.87

Statistical analysis and significance testing of serial analysis of gene expression data using a Poisson mixture model. BMC Bioinformatics (2007) 0.85

Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty. BMC Bioinformatics (2009) 0.85

Pairwise statistical significance and empirical determination of effective gap opening penalties for protein local sequence alignment. Int J Comput Biol Drug Des (2008) 0.84

Convergent Island Statistics: a fast method for determining local alignment score significance. Bioinformatics (2005) 0.84

PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance. Bioinformatics (2009) 0.83

Sequence-specific sequence comparison using pairwise statistical significance. Adv Exp Med Biol (2011) 0.77

Articles by these authors

RNAsnap™: a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria. Nucleic Acids Res (2012) 1.05

Development of a 5 year life expectancy index in older adults using predictive mining of electronic health record data. J Am Med Inform Assoc (2013) 1.03

Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing. Bioinformatics (2010) 0.99

DENSE: efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules. BMC Syst Biol (2011) 0.80

Assessing the efficacy of video versus direct laryngoscopy through retrospective comparison of 436 emergency intubation cases. J Anesth (2013) 0.80

A top-down approach to classify enzyme functional classes and sub-classes using random forest. EURASIP J Bioinform Syst Biol (2012) 0.80

Intraoperative diagnosis of acute pulmonary embolus by transesophageal echocardiogram. J Cardiothorac Vasc Anesth (2010) 0.79

Daytime and nighttime effects of brimonidine on IOP and aqueous humor dynamics in participants with ocular hypertension. J Glaucoma (2014) 0.78

Late failure rate of hearing preservation after middle fossa approach for resection of vestibular schwannoma. Otol Neurotol (2011) 0.77

Sequence-specific sequence comparison using pairwise statistical significance. Adv Exp Med Biol (2011) 0.77

Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel®Xeon Phi™ Coprocessor. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.77

Free-floating intracardiac mass after cardiopulmonary bypass for aortic valve replacement. Anesth Analg (2011) 0.75

BrainLAB interference with pulse oximetry during stereotactic brain biopsy. J Clin Anesth (2012) 0.75

Rare cause of light failure of a Macintosh 4 blade. J Clin Anesth (2012) 0.75

Echocardiography-based hemodynamic management of left ventricular diastolic dysfunction: a feasibility and safety study. Echocardiography (2014) 0.75

Hospital based prospective longitudinal clinical and immunologic study of 179 patients of primary anti-phospholipid syndrome. Int J Rheum Dis (2013) 0.75

Evaluation of the Masimo® Rainbow SET Radical-7 in a 6-month-old pediatric multivisceral organ transplant. J Anesth (2012) 0.75

Bulk oxygen tank vaporizer leak. J Clin Anesth (2012) 0.75

Improved Scaling of Molecular Network Calculations: The Emergence of Molecular Domains. J Phys Chem Lett (2016) 0.75

Rare cause of light failure in two Macintosh blades within 2 weeks. J Anesth (2010) 0.75