Parallel pairwise statistical significance estimation of local sequence alignment using Message Passing Interface library

Ankit Agrawal; Sanchit Misra; Daniel Honbo; Alok Choudhary

doi:10.1002/cpe.1798

Parallel pairwise statistical significance estimation of local sequence alignment using Message Passing Interface library

Concurrency and Computation Practice and Experience ◽

10.1002/cpe.1798 ◽

2011 ◽

Vol 23 (17) ◽

pp. 2269-2279 ◽

Cited By ~ 7

Author(s):

Ankit Agrawal ◽

Sanchit Misra ◽

Daniel Honbo ◽

Alok Choudhary

Keyword(s):

Sequence Alignment ◽

Message Passing ◽

Message Passing Interface ◽

Statistical Significance ◽

Local Sequence Alignment ◽

Local Sequence

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Pairwise Statistical Significance of Local Sequence Alignment Using Sequence-Specific and Position-Specific Substitution Matrices

IEEE/ACM Transactions on Computational Biology and Bioinformatics ◽

10.1109/tcbb.2009.69 ◽

2011 ◽

Vol 8 (1) ◽

pp. 194-205 ◽

Cited By ~ 17

Author(s):

A Agrawal ◽

Xiaoqiu Huang

Keyword(s):

Sequence Alignment ◽

Statistical Significance ◽

Local Sequence Alignment ◽

Substitution Matrices ◽

Local Sequence

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Par-PSSE: Software for Pairwise Statistical Significance Estimation in Parallel for Local Sequence Alignment

International Journal of Digital Content Technology and its Applications ◽

10.4156/jdcta.vol6.issue5.24 ◽

2012 ◽

Vol 6 (5) ◽

pp. 200-208 ◽

Cited By ~ 1

Author(s):

Yuhong Zhang ◽

Md. Mostofa Ali Patwary ◽

Sanchit Misra ◽

Ankit Agrawal ◽

Weikeng

Keyword(s):

Sequence Alignment ◽

Statistical Significance ◽

Local Sequence Alignment ◽

Local Sequence

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Pairwise statistical significance and empirical determination of effective gap opening penalties for protein local sequence alignment

International Journal of Computational Biology and Drug Design ◽

10.1504/ijcbdd.2008.022207 ◽

2008 ◽

Vol 1 (4) ◽

pp. 347 ◽

Cited By ~ 10

Author(s):

Ankit Agrawal ◽

Volker P. Brendel ◽

Xiaoqiu Huang

Keyword(s):

Sequence Alignment ◽

Statistical Significance ◽

Local Sequence Alignment ◽

Local Sequence ◽

Empirical Determination ◽

Gap Opening

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Pairwise statistical significance of local sequence alignment using multiple parameter sets

Proceeding of the 2nd international workshop on Data and text mining in bioinformatics - DTMBIO '08 ◽

10.1145/1458449.1458462 ◽

2008 ◽

Cited By ~ 2

Author(s):

Ankit Agrawal ◽

Xiaoqiu Huang

Keyword(s):

Sequence Alignment ◽

Statistical Significance ◽

Local Sequence Alignment ◽

Local Sequence ◽

Multiple Parameter

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A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

PLoS Computational Biology ◽

10.1371/journal.pcbi.1000069 ◽

2008 ◽

Vol 4 (5) ◽

pp. e1000069 ◽

Cited By ~ 191

Author(s):

Sean R. Eddy

Keyword(s):

Sequence Alignment ◽

Probabilistic Model ◽

Statistical Significance ◽

Local Sequence Alignment ◽

Local Sequence

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Pairwise Statistical Significance of Local Sequence Alignment Using Substitution Matrices with Sequence-Pair-Specific Distance

2008 International Conference on Information Technology ◽

10.1109/icit.2008.63 ◽

2008 ◽

Cited By ~ 3

Author(s):

Ankit Agrawal ◽

Xiaoqiu Huang

Keyword(s):

Sequence Alignment ◽

Statistical Significance ◽

Sequence Pair ◽

Local Sequence Alignment ◽

Substitution Matrices ◽

Local Sequence ◽

Specific Distance

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Efficient pairwise statistical significance estimation for local sequence alignment using GPU

2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) ◽

10.1109/iccabs.2011.5729885 ◽

2011 ◽

Cited By ~ 6

Author(s):

Yuhong Zhang ◽

Sanchit Misra ◽

Daniel Honbo ◽

Ankit Agrawal ◽

Wei-keng Liao ◽

...

Keyword(s):

Sequence Alignment ◽

Statistical Significance ◽

Local Sequence Alignment ◽

Local Sequence

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Assessing the Statistical Significance of Local Sequence Alignment Based on Transformation Score Matrix

Current Bioinformatics ◽

10.2174/157489312803901036 ◽

2012 ◽

Vol 7 (4) ◽

pp. 505-511 ◽

Cited By ~ 1

Author(s):

Juan Li ◽

Huisheng Fang

Keyword(s):

Sequence Alignment ◽

Statistical Significance ◽

Local Sequence Alignment ◽

Local Sequence ◽

Score Matrix

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Conservative, Non-conservative and Average Pairwise Statistical Significance of Local Sequence Alignment

2008 IEEE International Conference on Bioinformatics and Biomedicine ◽

10.1109/bibm.2008.19 ◽

2008 ◽

Cited By ~ 3

Author(s):

Ankit Agrawal ◽

Xiaoqiu Huang

Keyword(s):

Sequence Alignment ◽

Statistical Significance ◽

Local Sequence Alignment ◽

Local Sequence

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Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty

BMC Bioinformatics ◽

10.1186/1471-2105-10-s3-s1 ◽

2009 ◽

Vol 10 (S3) ◽

Cited By ~ 12

Author(s):

Ankit Agrawal ◽

Xiaoqiu Huang

Keyword(s):

Sequence Alignment ◽

Statistical Significance ◽

Empirical Justification ◽

Local Sequence Alignment ◽

Local Sequence ◽

Multiple Parameter

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