'Profile hmm' diaporamas de présentation

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Profile HMMs

Profile HMMs

Profile HMMs. Biology 162 Computational Genetics Todd Vision 16 Sep 2004. Outline. Profile HMMs generate MSAs States and transitions for Matches, Insertions, Deletions, Silent and Flanking states Statistics Null model, E values Training

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472 views • 33 slides
CSCE555 Bioinformatics

CSCE555 Bioinformatics

CSCE555 Bioinformatics. Lecture 6 Hidden Markov Models Meeting: MW 4:00PM-5:15PM SWGN2A21 Instructor: Dr. Jianjun Hu Course page: http://www.scigen.org/csce555. HAPPY CHINESE NEW YEAR. University of South Carolina Department of Computer Science and Engineering 2008 www.cse.sc.edu.

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594 views • 33 slides
CECS 694-04 Bioinformatics Journal Club Eric Rouchka, D.Sc. September 10, 2003

CECS 694-04 Bioinformatics Journal Club Eric Rouchka, D.Sc. September 10, 2003

SATCHMO: sequence alignment and tree construction using hidden Markov models Edgar, R.C. and Sjolander, K. Bioinformatics . 19 (11):1404-1411. CECS 694-04 Bioinformatics Journal Club Eric Rouchka, D.Sc. September 10, 2003. What is Multiple Sequence Alignment (MSA) ?.

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432 views • 29 slides
IMPROVED TECHNIQUES FOR THE IDENTIFICATION OF PSEUDOGENES

IMPROVED TECHNIQUES FOR THE IDENTIFICATION OF PSEUDOGENES

IMPROVED TECHNIQUES FOR THE IDENTIFICATION OF PSEUDOGENES. L. Coin and R. Durbin Wellcome Trust Sanger Institute. BIOINFORMATICS 2004 Presented by: Oscar Sanchez Plazas. Outline. Problem definition Previous works on pseudogene identification Proposed method Protein domain profile (Pfam)

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398 views • 23 slides
IMPROVED TECHNIQUES FOR THE IDENTIFICATION OF PSEUDOGENES

IMPROVED TECHNIQUES FOR THE IDENTIFICATION OF PSEUDOGENES

IMPROVED TECHNIQUES FOR THE IDENTIFICATION OF PSEUDOGENES. L. Coin and R. Durbin Wellcome Trust Sanger Institute. BIOINFORMATICS 2004 Presented by: Oscar Sanchez Plazas. Outline. Problem definition Previous works on pseudogene identification Proposed method Protein domain profile (Pfam)

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332 views • 23 slides
Profile Hidden Markov Models

Profile Hidden Markov Models

Profile Hidden Markov Models. Bioinformatics Fall-2004 Dr Webb Miller and Dr Claude Depamphilis Dhiraj Joshi Department of Computer Science and Engineering The Pennsylvania State University. Outline. Introduction to HMMs Profile HMMs

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407 views • 23 slides
Scoring Matrices

Scoring Matrices

Scoring Matrices. Scoring matrices, PSSMs, and HMMs. Reading: Ch 6.1. BIO520 Bioinformatics Jim Lund. Alignment scoring matrix. DNA matrix: A C G T A 5 -4 -4 -4 C -4 5 -4 -4 G -4 -4 5 -4 T -4 -4 -4 5. Alignment scoring matrix. Protein matrix:. Use of a scoring matrix.

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551 views • 23 slides
Applications of HMMs in Computational Biology

Applications of HMMs in Computational Biology

Applications of HMMs in Computational Biology. BMI/CS 576 www.biostat.wisc.edu/bmi576.html Colin Dewey cdewey@biostat.wisc.edu Fall 2010. The Gene Finding Task. Given: an uncharacterized DNA sequence

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365 views • 22 slides
RBP1 Splicing Regulation in Drosophila Melanogaster

RBP1 Splicing Regulation in Drosophila Melanogaster

RBP1 Splicing Regulation in Drosophila Melanogaster. 03-711 - Fall 2005 Jacob Joseph, Ahmet Bakan, Amina Abdulla. This presentation available at http://www.jjoseph.org/biology/. Alternative Splicing in Dros. RBP1 Regulation. Involved in dsx splicing and Rbp1 auto-regulation

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315 views • 18 slides
Ab Initio Profile HMM Generation

Ab Initio Profile HMM Generation

Ab Initio Profile HMM Generation. Sam Gross. STOLEN FROM BATZOGLOU LECTURE. D m-1. D m. D 1. D 2. BEGIN. END. I 0. I 1. I m-1. I m. M 1. M 2. M m. Profile HMMs. Each M state has a position-specific pre-computed substitution table

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Why predict RNA?

Why predict RNA?

DNA. cis- or trans-regulatory trans-regulatory Antisense RNA Riboswitches CRISPR etc. RNA. rRNA. mRNA. tRNA. PROTEIN. Why predict RNA?. Regulation. Protein Biosynthesis. Noncoding RNA. Traditional paradigm. Regulatory sRNA.

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244 views • 10 slides
Why predict RNA?

Why predict RNA?

DNA. cis- or trans-regulatory trans-regulatory Antisense RNA Riboswitches CRISPR etc. RNA. rRNA. mRNA. tRNA. PROTEIN. Why predict RNA?. Regulation. Protein Biosynthesis. Noncoding RNA. Traditional paradigm. Regulatory sRNA. Hypothesis:

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213 views • 10 slides

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