'Related sequences' diaporamas de présentation

NCBI Databases and Services

NCBI Databases and Services. GenBank largest sequence database Free public access to biomedical literature PubMed free Medline PubMed Central full text online access Entrez integrated molecular and literature databases BLAST highest volume sequence search service

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CS 5263 Bioinformatics

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Computational Genomics Lecture #3

Computational Genomics Lecture #3. Crash intro to ML Scoring functions and DNA and AAs Multiple sequence alignment. Background Readings : Chapters 2.5, 2.7 in the text book, Biological Sequence Analysis , Durbin et al., 2001.

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Multiple Sequence Alignment

Multiple Sequence Alignment. Julie Thompson Laboratory of Integrative Bioinformatics and Genomics IGBMC, Strasbourg, France julie@igbmc.fr. Multiple Sequence Alignment. Introduction: what is a multiple alignment? Multiple alignment construction Traditional approaches: optimal, progressive

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Computational Genomics Lecture #2b

Computational Genomics Lecture #2b. Scoring functions and DNA and AAs Multiple sequence alignment. Background Readings : Chapters 2.5, 2.7 in the text book, Biological Sequence Analysis , Durbin et al., 2001.

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LSM2104 Part II Lectures 3 and 4

LSM2104 Part II Lectures 3 and 4. Tan Tin Wee Dept of Biochemistry NUS. Topics. Derivation of PAM and BLOSUM and Scoring Matrices Basic Introduction to Dynamic Programming Techniques Details of Needleman-Wunsch and Smith-Waterman Algoriths FASTA and BLAST Heuristics

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Introduction to Sequence Analysis Software & Data Libraries

Introduction to Sequence Analysis Software & Data Libraries. Alex Ropelewski ropelews@psc.edu MARC: Developing Bioinformatics Programs July 17-28, 2006. Why Sequence Analysis.

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Introduction to Sequence Analysis

Introduction to Sequence Analysis. MARC: Developing Bioinformatics Programs July, 2008 Alex Ropelewski ropelews@psc.edu Hugh Nicholas nicholas@psc.edu. Bioinformatics.

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Fasta, Blast, Probabilities

Fasta, Blast, Probabilities. Reminder. Last classes we discussed dynamic programming algorithms for global alignment local alignment Multiple alignment All of these assumed a scoring rule: that determines the quality of perfect matches, substitutions, insertions, and deletions.

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Class 3: Estimating Scoring Rules for Sequence Alignment

Class 3: Estimating Scoring Rules for Sequence Alignment. Reminder. Last class we discussed dynamic programming algorithms for global alignment local alignment

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Class 3: Estimating Scoring Rules for Sequence Alignment

Class 3: Estimating Scoring Rules for Sequence Alignment. Reminder. Last class we discussed dynamic programming algorithms for global alignment local alignment

461 views • 35 slides

School B&I TCD Bioinformatics

School B&I TCD Bioinformatics. Database homology searching May 2010. Why search a Database. To find homologous sequences to your unknown to determine function To find other related sequences to do evolutionary studies (trees) or to make specialised database (nematode 16sRNA)

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Sequence Alignment II Lecture #3

Sequence Alignment II Lecture #3. Background Readings : Chapters 2.5, 2.7 in the text book, Biological Sequence Analysis , Durbin et al., 2001. Chapters 3.5.1- 3.5.3, 3.6.2 in Introduction to Computational Molecular Biology , Setubal and Meidanis, 1997.

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BLAST

BLAST. Sequence alignment, E-value & Extreme value distribution. Database searching. Using pairwise alignments to search databases for similar sequences. Query sequence. Database. Database sizes. PDB: 169,581 sequences; 39,601,444 total letters

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Rationale for searching sequence databases

Rationale for searching sequence databases. June 25, 2003 Writing projects due July 11 Learning objectives- FASTA and BLAST programs. Psi-Blast Workshop-Use of Psi-BLAST to determine sequence similarities. Use BLASTx to gain information on gene structure. FASTA (Pearson and Lipman 1988).

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Comparing Protein Sequences

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BLAST

BLAST. Anders Gorm Pedersen & Rasmus Wernersson. Database searching. Using pairwise alignments to search databases for similar sequences. Query sequence. Database. Database searching.

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Pairwise Sequence Alignment (cont.)

Pairwise Sequence Alignment (cont.). (Lecture for CS397-CXZ Algorithms in Bioinformatics) Feb. 6, 2004 ChengXiang Zhai Department of Computer Science University of Illinois, Urbana-Champaign. 4 Basic Questions in Pairwise Alignment. (Modeling evolution). Q1: How should we define s?.

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Abstract

Identification of Oral Taxa from Rare Phyla/Candidate Divisions Anuj Camanocha and Floyd E. Dewhirst Harvard School of Dental Medicine , Boston, and The Forsyth Institute, Cambridge, Massachusetts, USA. 1119. Anuj. Floyd. Results. Abstract. Figures and Tables.

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