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Smith–Waterman algorithm
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41	PRACE SHAPE and NSilico pool HPC knowledge to develop faster sequencing methods Via PRACE SHAPE NSilico teamed up with computational experts from CINES (France) and ICHEC (Ireland) to address the key problem of rapid ali Add to Reading List Source URL: www.prace-ri.eu Language: English - Date: 2014-10-13 07:49:39 Applied mathematics Partnership for Advanced Computing in Europe Bioinformatics Mathematical and theoretical biology Parallel computing Computational science Irish Centre for High-End Computing Smith–Waterman algorithm Multi-core processor Science Computational phylogenetics Computing
42	Hardware Accelerated Novel Optical De Novo Assembly for Large-Scale Genomes Pingfan Meng∗† , Matthew Jacobsen∗† , Motoki Kimura∗‡ , Vladimir Dergachev§ , Thomas Anantharaman§ , Michael Requa§ and Ryan Kast Add to Reading List Source URL: kastner.ucsd.edu Language: English - Date: 2014-06-30 10:30:54 Computational phylogenetics Applied mathematics Graphics hardware Video cards GPGPU Smith–Waterman algorithm CUDA Sequence assembly Matrix Dynamic programming Bioinformatics Science
43	AUTOMATIC ALIGNMENT OF MUSIC PERFORMANCES WITH STRUCTURAL DIFFERENCES Maarten Grachten1 Martin Gasser1 1 Austrian Research Institute for Artificial Intelligence (OFAI), Vienna, Austria Add to Reading List Source URL: phenicx.upf.edu Language: English - Date: 2015-01-15 05:32:07 Bioinformatics Science Dynamic time warping Time series analysis Needleman–Wunsch algorithm Sequence alignment Smith–Waterman algorithm Jensen–Shannon divergence Distance matrix Dynamic programming Computational phylogenetics Statistics
44	ART-A software guide version 0.1 Daniel Struck 1 Add to Reading List Source URL: arta.retrovirology.lu Language: English - Date: 2013-02-13 06:44:50 Computational science BioJava FASTA format FASTA Sequence alignment Smith–Waterman algorithm Trimming Bioinformatics Science Computational phylogenetics
45	"Selecting the Right Similarity-Scoring Matrix". In: Current Protocols in Bioinformatics Add to Reading List Source URL: faculty.virginia.edu Language: English - Date: 2014-05-12 09:11:44 Science Sequence alignment BLOSUM Smith–Waterman algorithm FASTA BLAST Substitution model Matrix Nucleic acid sequence Bioinformatics Computational phylogenetics Biology
46	Flexible sequence similarity searching with the FASTA3 program package William R. Pearson Department of Biochemistry, Add to Reading List Source URL: faculty.virginia.edu Language: English - Date: 1998-09-14 11:00:38 Computational science FASTA BLAST Sequence alignment Sequence database Sequence analysis Smith–Waterman algorithm Substitution matrix Warren Gish Bioinformatics Science Computational phylogenetics
47	An Introduction to Sequence Similarity (“Homology”) Searching UNIT 3.1 William R. Pearson1 Add to Reading List Source URL: faculty.virginia.edu Language: English - Date: 2014-05-12 09:11:44 Biology Sequence alignment Multiple sequence alignment FASTA BLAST Smith–Waterman algorithm Homology InterPro Sequence database Bioinformatics Science Computational phylogenetics
48	Sequence comparison using a relational database approach Andre Bergholz Institut fur Informatik Humboldt-Universitat zu Berlin Unter den Linden 6 D[removed]Berlin, Germany Add to Reading List Source URL: www.dbis.informatik.hu-berlin.de Language: English - Date: 2005-07-20 02:26:58 Computational science BLAST Smith–Waterman algorithm Sequence alignment Sequence analysis Nucleic acid sequence Sequence database STING DNA Bioinformatics Science Computational phylogenetics
49	Sketch of the Blast Approach When comparing two sequences, the various versions of the Blast program perform some combination of the following steps. 1. “Word hits” are identified. By word we mean a contiguous segmen Add to Reading List Source URL: globin.cse.psu.edu Language: English - Date: 2001-09-18 09:36:52 BLAST Public domain software Computational science Smith–Waterman algorithm Position-specific scoring matrix Warren Gish Sequence alignment Science Bioinformatics Computational phylogenetics
50	RC454 USERS GUIDE General Description RC454 is a tool to clean 454 reads based on their alignment to a reference consensus assembly. The correction process is aggressive, and as such requires an assembly that is high Add to Reading List Source URL: www.broadinstitute.org Language: English - Date: 2012-11-08 17:47:42 FASTQ format FASTA format Sequence assembly FASTA Perl DNA sequencing 454 Life Sciences Diff Smith–Waterman algorithm Bioinformatics Computing Software