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Smith–Waterman algorithm
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#	Item
1	Today’s Lecture • Edit graph & alignment algorithms – Smith-Waterman algorithm – Needleman-Wunsch algorithm • Local vs global Add to Reading List Source URL: bozeman.mbt.washington.edu Language: English - Date: 2018-01-26 14:03:03
2	A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation Sean R. Eddy* Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, United States of Ameri Add to Reading List Source URL: selab.janelia.org Language: English - Date: 2014-09-02 13:41:13 Statistics Sequence alignment HMMER BLAST Hidden Markov model Smith–Waterman algorithm BLOSUM Pfam Stochastic context-free grammar Bioinformatics Science Computational phylogenetics
3	A Bioinformatics Approach to 3D Shape Matching Manuele Bicego(B) , Stefano Danese, Simone Melzi, and Umberto Castellani Dipartimento di Informatica, University of Verona, Strada le Grazie 15, 37134 Verona, Italy manuele. Add to Reading List Source URL: profs.sci.univr.it Language: English - Date: 2015-06-16 09:42:08 Biology Sequence alignment Sequence analysis BLAST Smith–Waterman algorithm DNA Nucleic acid sequence Needleman–Wunsch algorithm Structural alignment Computational phylogenetics Science Bioinformatics
4	Sequence Alignment Guided By Common Motifs Described By Context Free Grammars Abdullah N. Arslan Department of Computer Science University of Vermont Burlington, VT 05405, USA Add to Reading List Source URL: www.biotconf.org Language: English - Date: 2014-05-21 17:42:43 Science Mathematics Sequence alignment Needleman–Wunsch algorithm Smith–Waterman algorithm Structural alignment Multiple sequence alignment Sequence motif Nucleic acid sequence Computational phylogenetics Bioinformatics Dynamic programming
5	Protein Engineering vol.12 no.5 pp.387–394, 1999 PSIC: profile extraction from sequence alignments with position-specific counts of independent observations Shamil R.Sunyaev1,2,3, Frank Eisenhaber1,2,4, Add to Reading List Source URL: genetics.bwh.harvard.edu Language: English - Date: 2004-02-17 17:34:00 Computational science Sequence alignment BLAST Substitution matrix Multiple sequence alignment STING Smith–Waterman algorithm Threading Amino acid Bioinformatics Science Computational phylogenetics
6	2014 22nd International Conference on Pattern Recognition S-BLOSUM: classiﬁcation of 2D shapes with biological sequence alignment Pietro Lovato∗ , Alessio Milanese† , Cesare Centomo† , Alejandro Giorgetti† , M Add to Reading List Source URL: profs.sci.univr.it Language: English - Date: 2015-06-16 09:42:08 Biology BLOSUM Substitution matrix Sequence alignment Smith–Waterman algorithm Multiple sequence alignment BLAST Nucleic acid sequence Matrix Bioinformatics Computational phylogenetics Science
7	Genome InformaticsPages) Add to Reading List Source URL: selab.janelia.org Language: English - Date: 2014-09-02 13:40:00 HMMER Sequence alignment FASTA BLAST Sequence analysis Hidden Markov model Smith–Waterman algorithm BLOSUM Homology modeling Bioinformatics Science Computational phylogenetics
8	The Partition Function Variant of Sankoff ’s Algorithm Ivo L. Hofacker1 and Peter F. Stadler1,2 1 Institut f¨ Add to Reading List Source URL: www.bioinf.uni-leipzig.de Language: English - Date: 2004-01-30 07:21:50 Genetics Sequence alignment Dynamic programming Multiple sequence alignment Nucleic acid structure prediction T-Coffee Hidden Markov model Smith–Waterman algorithm Nucleic acid sequence Computational phylogenetics Bioinformatics Science
9	Vol. 27 no, pages 2433–2434 doi:bioinformatics/btr368 BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Add to Reading List Source URL: bioinformatics.oxfordjournals.org Language: English Applied mathematics BLAST Sequence alignment Smith–Waterman algorithm Seed Algorithm Yass Computational phylogenetics Science Bioinformatics
10	Parallel-ProBiS: Fast Parallel Algorithm for Local Structural Comparison of Protein Structures and Binding Sites Janez Konc,1 Matjaž Depolli,2 Roman Trobec,2 Kati Rozman,1 Dušanka Janežič1,* 1 Add to Reading List Source URL: www-e6.ijs.si Language: English - Date: 2013-08-01 05:14:14 Protein methods Bioinformatics Structural alignment Computational phylogenetics Speedup Message Passing Interface Distributed computing Computer cluster Smith–Waterman algorithm Computing Parallel computing Computer programming

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