'Multiple alignment' presentation slideshows

Section 9 Resolving Taxonomic Uncertainties & Defining Management Units

Section 9 Resolving Taxonomic Uncertainties & Defining Management Units. The taxonomic status of, and relationships among many taxa are unresolved. In conservation, many erroneous decisions may result if the taxonomic status of populations is not correctly assigned, such as:.

1.57k views • 110 slides

Protein Structure

Protein Structure. IST 444. Protein Chemistry Basics. Proteins are polymers consisting of amino acids linked by peptide bonds Each amino acid consists of: a central carbon atom an amino group NH 2 a carboxyl group COOH a side chain (R group)

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Phylogenetic Tree Reconstruction

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Multiple Sequence Alignment

Multiple Sequence Alignment. Terminology. Motif: the biological object one attempts to model - a functional or structural domain, active site, phosphorylation site etc. Pattern: a qualitative motif description based on a regular expression-like syntax

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Hidden Markov Models

Hidden Markov Models. CG -Islands. Given 4 nucleotides: probability of occurrence is ~ 1/4. Thus, probability of occurrence of a dinucleotide is ~ 1/16. However, the frequencies of dinucleotides in DNA sequences vary widely. In particular, CG is typically underepresented

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Bioinformatics Algorithms and Data Structures

Bioinformatics Algorithms and Data Structures. Chapter 14.1-5: Multiple String Comparisons Lecturer: Dr. Rose Slides by: Dr. Rose March 1, 2007. Multiple String Comparisons. Q: Why are we interesting in multiple string comparisons? A: At one level we are data-mining.

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Homology Modeling of Proteins

Homology Modeling of Proteins. Abhishek Tripathi Biomedicum, Helsinki. Computational methods for Protein Structure Prediction. Homology or Comparative Modeling Fold Recognition or threading Methods Ab initio methods that utilize knowledge-based information

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Computers and Programming for Biologists

Computers and Programming for Biologists. What is Bioinformatics?. The use of information technology to collect, analyze, and interpret biological data. An ad hoc collection of computing tools that are used by molecular biologists to manage research data. Computational algorithms

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Efficient Estimation of Emission Probabilities in profile HMM

Efficient Estimation of Emission Probabilities in profile HMM. By Virpi Ahola et al Reviewed By Alok Datar. Index. Motivation Introduction Method Simulation Results Conclusion. 1. Motivation. Drawbacks of HMM is that conserved amino acids are not emphasized.

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Molecular Replacement

Molecular Replacement Ronan Keegan Molecular Replacement and the Phase problem

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Molecular Replacement

Molecular Replacement. Ronan Keegan. Molecular Replacement and the Phase problem.

865 views • 29 slides

Phylogenetic Analysis

Phylogenetic Analysis. General comments on phylogenetics. Phylogenetics is the branch of biology that deals with evolutionary relatedness Uses some measure of evolutionary relatedness: e.g., morphological features.

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Roadmap

Roadmap. The topics: basic concepts of molecular biology more on Perl overview of the field biological databases and database searching sequence alignments phylogenetics structure prediction microarray data analysis. Sequence alignments. Introduction What is an alignment?

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Bioinformatics: A New Vision for Academics

Bioinformatics: A New Vision for Academics . University of Michigan - Flint Computer Science Department. 2 nd International Conference on Frontiers of Information Technology (FIT) 2006 Islamabad Pakistan December 20 - 21, 2006. Mudasser F. Wyne, Ph.D. Computer Science.

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Domains

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Hidden Markov Modeling, Multiple Alignments and Structure

Hidden Markov Modeling, Multiple Alignments and Structure Bioinformatic Modeling Techniques Student: Patricia Pearl The basic notion of a hidden Markov model was covered during the class lectures and in our midterm.

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BLAST

BLAST. Using online BLAST. database type. from Bio.Blast import NCBIWWW result_handle = NCBIWWW.qblast (" blastn ", " nt ", "8332116"). sequence. Blast program. or. from Bio.Blast import NCBIWWW from Bio import SeqIO record = SeqIO.read (" m_cold.fasta ", format=" fasta ")

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Overview of sequence database searching techniques and multiple alignment

Overview of sequence database searching techniques and multiple alignment. May 1, 2001 Quiz on May 3-Dynamic programming-Needleman-Wunsch method

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Bioinformatics and Genome Data Analysis

Bioinformatics and Genome Data Analysis. Fredj Tekaia Institut Pasteur tekaia@pasteur.fr. Bioinformatics and Genome Data Analysis. This advanced course aims at bringing multidisciplinary scientists around : a) What we learned from completely sequenced genomes. (Conferences: 1/2 time)

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Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments

Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments. Olivier Poirot, Eamonn O'Toole and Cedric Notredame Nucleic Acids Research, 31, 3503-3506 (2003) July 22, 2003 Park, Ji-Yoon. Abstract. Tcoffee@igs

270 views • 9 slides