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PatternHunter: faster and more sensitive homology search By Bin Ma, John Tromp and Ming Li B92902019 B92902033 B92902039
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Mega-BLAST uses seeds of length 28. PatternHunter uses 'spaced seeds' ... (homology identity = 0.7, homology length=64) 111011001011010111, 1111000100010011010111, ...
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Problem: Find all highly similar segments (called homologies) ... Smith-Waterman Algorithm --- dynamic programming algorithm --- output optimal local alignments ...
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Bioinformatics and Computational Molecular Biology (Fall 2005) ... Bioinformatics and Computational Molecular Biology (Fall 2005): Representation ...
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BLASTP, BLASTN, TBLAST, BLASTX, BLAT, BLASTZ, MegaBLAST, PsiBLAST, PhiBLAST. Others ... BLAT, BLASTZ, MegaBLAST. FLASH, PatternHunter, SSAHA, SENSEI, WABA, ...
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Filtering is based on the observation that a good alignment usually includes ... The idea of filtration was used in FASTA, BLAST, BLAT, and PatternHunter. ...
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Combinatorial Pattern Matching
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Mouse and Human Genomes: A First Look. Michael Kamal ... Mouse Genome: Arachne Assembly. Emphasize dramatic increase in supercontig size ...
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An Empirical Study of Choosing Efficient Discriminative Seeds for Oligonucleotide Design Won-Hyong Chung and Seong-Bae Park Dept. of Computer Engineering
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This leads us to a different problem, the Pattern Matching Problem ... When threading is 'complete,' we've found a pattern in the text ...
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... Needleman-Wunsch global alignment algorithm 1981: Smith-Waterman local alignment algorithm 1985: FASTA 1990: BLAST (basic local alignment search tool) ...
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Modern Homology Search Ming Li Canada Research Chair in Bioinformatics Computer Science. U. Waterloo I want to show you how one simple theoretical idea can make big ...
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Nicole Stange-Thomann. Toby Bloom. Jill Mesirov. Bruce Birren. Chad ... Webb Miller, PSU. Ross Hardison, PSU. Michael Brent, WU. British Columbia. Marco Marra ...
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DIY: download and compare sequences of the same protein in 20 different mammals. ... DIY: Experiment the sensitivity comparison between spaced seeds and BLAST seed. ...
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L3: Blast: Local Alignment and other flavors
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What is the probability that some position i has a match. ... Exact match of a short query substring to ... Scan the database for exact match to all such words ...
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Title: Viaggio nel mondo dei Genomi Subject: seminario di bioinformatica Author: Giuseppe Cazzato e Alice Fulgido Last modified by: fremyd Created Date
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Our goal is to make an automaton that accepts all strings which contain a string ... Substring automaton. We started ... Suppose R is described by automaton A ...
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Title: PowerPoint Presentation Author: heringa Last modified by: heringa Created Date: 2/20/2003 6:08:47 PM Document presentation format: On-screen Show (4:3)
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Below is a chart of three hosts used for cloning fragments and the sizes of ... This method is also called 'Double-Barrelled WGS' ...
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There are two official language in this class. One is English. The other is ... Michael S. Waterman. 22. Dept. of Computer Science & Information Engineering ...
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Chaining Chain Letters. Charles H. Bennett collected 33 copies 1980--1997. ... with love all things are possible. this paper has been sent to you for good luck. ...
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Title: PowerPoint Presentation Author: heringa Last modified by: heringa Created Date: 2/20/2003 6:08:47 PM Document presentation format: On-screen Show (4:3)
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Therefore, when PTM is present, one has to try different PTM possibilities to ... I plan to teach SPIDER in my Advanced Bioinformatics class. ...
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Q: What is the score of the best alignment of the two strings s and t? ... Concatenate all of the database sequences to form one giant sequence. ...
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Heuristic approach based on Smith Waterman algorithm. Finds ... Crab-eating macaque CDC20 mRNA. Default human database. New output display. NCBI FieldGuide ...
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... and data visualization/ analysis tools such as Spotfire Solid understanding of relational databases and familiarity with Oracle and/ or SQL server Good ...
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NCBI FieldGuide. A Field Guide. part 2. February 14, 2006 ... Primate division gbdiv pri[prop] EST division gbdiv est[prop] NCBI FieldGuide. Molecule Queries ...
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... WU-Blast, psi-Blast, SIM, BLAT, MUMmer, Quasar, etc. ... Suffix tree: MUMmer, Quasar, REPuter. Only good for precise matches, highly similar sequences. ...
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When the genomic DNA sequences of closely related organisms become ... other implementations: QUASAR, REPuter. 4. Lecture WS 2003/04. Bioinformatics III. 16 ...
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Each substructure is optimal. (Principle of optimality) 1. optimal substructures. 2. overlapping subproblems. Subproblems are dependent. ...
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Heuristic approach based on Smith Waterman algorithm. Finds ... The Tetrapod Albumin Regions. Trace Archive Megablast. Platypus WGS trace Hits. Platypus traces ...
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Alignement local avec chaque s quence d'ADN (GenBank) ou de prot ines (Swiss-Prot) ... Score d'un alignement multipli par une valeur entre 0 et 1 en fonction de la ...
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