'Cpg islands' diaporamas de présentation

CS5263 Bioinformatics

CS5263 Bioinformatics. Lecture 11: Markov Chain and Hidden Markov Models. In the next few lectures. Hidden Markov Models The theory Probabilistic treatment of sequence alignments using HMMs Application of HMMs to biological sequence modeling and discovery of features such as genes.

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Markov Chains

Markov Chains. and hidden Markov models. Motivation - CpG islands :. CpG is a pair of nucleotides C and G , appearing successively , in this order, along one DNA strand. CpG islands are particular short subsequences in them the couple CpG is more frequent.

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Parameter Estimation For HMM Lecture #7

Parameter Estimation For HMM Lecture #7. Background Readings : Chapter 3.3 in the text book, Biological Sequence Analysis , Durbin et al., 2001. M. M. M. M. S 1. S 2. S L-1. S L. T. T. T. T. x 1. x 2. X L-1. x L. Reminder: Hidden Markov Model.

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Introduction of Dr. Yongfeng Shang

Introduction of Dr. Yongfeng Shang. Jin-Qiu Zhou jqzhou@sibs.ac.cn Shanghai Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences. Epigenetics?. Greek, epi = above, upon; Epigenetics=above genetics

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Markov Chains Lecture #5

Markov Chains Lecture #5. Background Readings : Durbin et. al. Section 3.1, . Dependencies along the genome. In previous classes we assumed every letter in a sequence is sampled randomly from some distribution q( ? ) over the alpha bet {A,C,T,G}.

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Algorithms in Computational Biology

Algorithms in Computational Biology. Markov Chains and Hidden Markov Model. Example: CpG Islands. Dinucleotide CG ( CpG to distinguish it from C-G base pair) C within CG is typically methylated Methyl-C is more likely to mutate to T

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BB30055: Genes and genomes

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A modeling Example

A+. C+. G+. T+. A-. C-. G-. T-. A modeling Example. CpG islands in DNA sequences. Methylation & Silencing. One way cells differentiate is methylation Addition of CH 3 in C-nucleotides Silences genes in region CG (denoted CpG) often mutates to TG, when methylated

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CSCE555 Bioinformatics

CSCE555 Bioinformatics. Lecture 8 Gene Finding 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. Outline.

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Human Genome Project

Human Genome Project. Janice S. Dorman, PhD University of Pittsburgh School of Nursing. Lesson One. History of the Human Genome Project. Human Genome Project, 1984-86. DOE was interested in genetic research regarding health effects from radiation and chemical exposure

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Hidden Markov Models

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Hidden Markov Models (HMMs)

Hidden Markov Models (HMMs). (Lecture for CS498-CXZ Algorithms in Bioinformatics) Oct. 27, 2005 ChengXiang Zhai Department of Computer Science University of Illinois, Urbana-Champaign. Motivation: the CpG island problem. Methylation in human genome

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RNA interference, and DNA methylation RCOOH ?RCOOCH3

Why CpG islands? CSE, Marmara University mimoza.marmara.edu.tr/~m.sakalli/cse546 Including some slights of Papoulis. These notes will be further modified. Dec/15/09 Notes on probability are from A. Papoulis and S. U. Pillai,. RNA interference, and DNA methylation RCOOH ?RCOOCH3.

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Hidden Markov Models (HMMs)

Hidden Markov Models (HMMs). (Lecture for CS498-CXZ Algorithms in Bioinformatics) Oct. 27, 2005 ChengXiang Zhai Department of Computer Science University of Illinois, Urbana-Champaign. Motivation: the CpG island problem. Methylation in human genome

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Hidden Markov Models

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Major insights from the HGP on

Major insights from the HGP on. Gene content Proteome content SNP identification Distribution of GC content CpG islands Recombination rates Repeat content. Nature (2001) 15 th Feb Vol 409 special issue; pgs 814 & 875-914. 1) Gene content.

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DNA Analysis Part II

DNA Analysis Part II. Amir Golnabi ENGS 112 Spring 2008. What we saw in part I: Markov Chain DNA and Modeling Markovian Models for DNA Sequences HMM for DNA Sequences Part II: DNA Methylation and CpG islands Markov Chain Model Hidden Markov Model Finding the State Path

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Additional file 6. T-DMRs within the Hoxa gene cluster.

Additional file 6. T-DMRs within the Hoxa gene cluster. CpG islands. a1 a2 BC094279 NM175261 a3 a5 a6 a7 a9 a10 a11 a13. Transcripts. Transcription direction. Liver. Brain. Heart. Testis. Methylation Peak Number.

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Introduction:

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