Gene Prediction: Similarity-Based Approaches

Jul 16, 2012

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Outline. . The idea of similarity-based approach to gene prediction Exon Chaining ProblemSpliced Alignment ProblemGene prediction tools. Using Known Genes to Predict New Genes. Some genomes may be well-studied, with many genes having been experimentally verified.Closely-related organisms may h

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Gene Prediction: Similarity-Based Approaches

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Presentation Transcript

1. Gene Prediction:Similarity-Based Approaches

2. Outline

Gene Prediction: Similarity-Based Approaches

Gene Prediction: Similarity-Based Approaches. Outline. The idea of similarity-based approach to gene prediction Exon Chaining Problem Spliced Alignment Problem Gene prediction tools. Using Known Genes to Predict New Genes.

720 views • 44 slides

Chemical similarity with Toxmatch 1.03 and Ambit Discovery

2. Chemical similarity assessment using Ambit Database. Exact substructure search based on 2D Structural Similarity search (various methods) Criteria on descriptors Based on mechanistic understanding Verhaar scheme. 3. Another view on Similarity assessments with Toxmatch and Ambit Discovery.

759 views • 30 slides

Image Similarity

Image Similarity. Longin Jan Latecki CIS Dept. Temple Univ., Philadelphia latecki@temple.edu. Image Similarity. Image based, e.g., difference of values of corresponding pixels Histogram based Based on similarity of objects contained in images, requires image segmentation.

397 views • 11 slides

3. Genome Annotation: Gene Prediction (II)

3. Genome Annotation: Gene Prediction (II). Gene Prediction: Computational Challenge. Gene : A sequence of nucleotides coding for protein Gene Prediction Problem : Determine the beginning and end positions of genes in a genome. Eukaryotic gene finding.

627 views • 40 slides

Similarity-based Classifiers: Problems and Solutions

Similarity-based Classifiers: Problems and Solutions. Classifying based on similarities :. Van Gogh. Monet. Van Gogh Or Monet ?. the Similarity-based Classification Problem. (paintings). (painter). the Similarity-based Classification Problem.

754 views • 74 slides

Chapter 8 Nearest Neighbor Approaches: Memory-Based Reasoning and Collaborative Filtering

Chapter 8 Nearest Neighbor Approaches: Memory-Based Reasoning and Collaborative Filtering. Nearest Neighbor Approaches. Based on the concept of similarity Memory-Based Reasoning (MBR) – results are based on analogous situations in the past

427 views • 24 slides

Structure Prediction

Structure Prediction. Tertiary protein structure: protein folding. Three main approaches: [1] experimental determination (X-ray crystallography, NMR) [2] Comparative modeling (based on homology) [3] Ab initio (de novo) prediction (Dr. Ingo Ruczinski at JHSPH) .

485 views • 29 slides

Genome Analysis & Gene Prediction

Genome Analysis & Gene Prediction. Overview about Genes. Gene : whole nucleic acid sequence necessary for the synthesis of a functional protein (or functional RNA) A human cell contains approximately 23,000 genes.

530 views • 28 slides

Maize genome annotation project Agry 60000 group 2

Maize genome annotation project Agry 60000 group 2. Karthik Padmanabhan Shuai Chen Shaylyn Wiarda. 12/06/12. workflow. MegaBLAST Gene Prediction on unmasked sequence AUGUSTUS FGENESH GeneMark CpG island prediction Repeat Masker Gene Prediction on masked sequence AUGUSTUS FGENESH

279 views • 12 slides

Gene Prediction: Statistical Approaches

Gene Prediction: Statistical Approaches. An Introduction to Bioinformatics Algorithms (Jones and Pevzner) www.bioalgorithms.info. Gene Prediction: Computational Challenge. Gene : A sequence of nucleotides coding for protein

682 views • 49 slides

Gene Prediction

Gene Prediction. Preliminary Results Computational Genomics February 20, 2012. ab initio Gene Prediction. Using Glimmer3, RAST, Prodigal and GenemarkS. Prodigal. lack of complexity(no Hidden Markov Model, no Interpolated Markov Model). based on dynamic programming.

783 views • 49 slides

Gene Prediction: Similarity-Based Approaches

Gene Prediction: Similarity-Based Approaches. Outline. Introduction Exon Chaining Problem Spliced Alignment Gene Prediction Tools. Section 1: Introduction. Similarity-Based Approach to Gene Prediction. Some genomes may be well-studied, with many genes having been experimentally verified.

775 views • 53 slides

Introduction to the HWRF-based Ensemble Prediction System

Introduction to the HWRF-based Ensemble Prediction System. Zhan Zhang and HWRF Team. Outline. Introduction to ensemble prediction system What and why ensemble prediction Approaches to ensemble prediction Hurricane ensemble prediction HWRF-based EPS Methodology;

586 views • 36 slides

C omputational ncRNA gene finding (& nc RNA structure prediction)

C omputational ncRNA gene finding (& nc RNA structure prediction). nc RNA structure prediction (& computational ncRNA gene finding). Liming Cai. (BINF8210@UGA, Fall 2010). Non-coding RNAs. Functions other than coding proteins, e.g., structural, catalytic, and regulatory factors

1.09k views • 95 slides

Computational Approaches to Receptor Structure Prediction

Computational Approaches to Receptor Structure Prediction. Uğur Sezerman Biological Sciences and Bioengineering Program Sabancı University, Istanbul. Determining Protein Structure. There are O(100,000) distinct proteins in the human proteome.

700 views • 56 slides

Feature Based Similarity

Christian Böhm, Bernhard Braunmüller, Florian Krebs, and Hans-Peter Kriegel, University of Munich Epsilon Grid Order: An Algorithm for the Similarity Join on Massive High-Dimensional Data. Feature Based Similarity. Simple Similarity Queries. Specify query object and

323 views • 17 slides

Wellcome Trust Workshop Working with Pathogen Genomes Module 2 Gene Prediction

Wellcome Trust Workshop Working with Pathogen Genomes Module 2 Gene Prediction. The Annotation Process. DNA SEQUENCE. Useful Information. ANNALYSIS SOFTWARE. Annotator. Gene finding. Sequence. sequence alignment to related gene (e.g. orthologue). base composition.

580 views • 44 slides

gene prediction

gene prediction. roderic guigó i serra IMIM/UPF/CRG. number of genes in chromosome 22. initial annotation 545 Dunham et al., 1999 genscan+RT-PCR 590 Das et al., 2001 genscan+microarrays 730 Shoemaker et al., 2001 reviewed annotation 726 chr22 team, sanger, 2001

514 views • 25 slides

Gene prediction and HMM Computational Genomics 2005/6 Lecture 9b

Gene prediction and HMM Computational Genomics 2005/6 Lecture 9b. Slides taken (and rapidly mixed) from William Stafford Noble, Larry Hunter, and Eyal Pribman. Partially modified by Benny Chor. Annotation of Genomic Sequence.

825 views • 69 slides

Lecture 22 Word Similarity

Lecture 22 Word Similarity. CSCE 771 Natural Language Processing. Topics word similarity Thesaurus based word similarity I ntro. Distributional based word similarity Readings: NLTK book Chapter 2 ( wordnet ) Text Chapter 20. April 8, 2013. Overview. Last Time (Programming)

1.02k views • 64 slides

Alarm-based prediction:

Alarm-based prediction:. goals, construction and quality assessment. Ilya Zaliapin Department of Mathematics and Statistics University of Nevada, Reno. Thanks: V. Keilis-Borok, G. Molchan, Y. Kagan, J. Zechar. Global Collaboration and Testing Meeting, April 21, 2008. Prediction goal.

242 views • 10 slides

Improving gene expression similarity measurement using pathway-based analytic dimension

Improving gene expression similarity measurement using pathway-based analytic dimension. Changwon Keum BMDRC. Accumulated gene expression data in public repository. GEO, NCBI. Search the database. * Search by annotation. * Search by contents. Dataset vs. individual sample( profile).

271 views • 14 slides

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Gene Prediction: Similarity-Based Approaches

Gene Prediction: Similarity-Based Approaches

Presentation Transcript

Gene Prediction: Similarity-Based Approaches

Chemical similarity with Toxmatch 1.03 and Ambit Discovery

Image Similarity

3. Genome Annotation: Gene Prediction (II)

Similarity-based Classifiers: Problems and Solutions

Chapter 8 Nearest Neighbor Approaches: Memory-Based Reasoning and Collaborative Filtering

Structure Prediction

Genome Analysis &amp; Gene Prediction

Maize genome annotation project Agry 60000 group 2

Gene Prediction: Statistical Approaches

Gene Prediction

Gene Prediction: Similarity-Based Approaches

Introduction to the HWRF-based Ensemble Prediction System

C omputational ncRNA gene finding (&amp; nc RNA structure prediction)

Computational Approaches to Receptor Structure Prediction

Feature Based Similarity

Wellcome Trust Workshop Working with Pathogen Genomes Module 2 Gene Prediction

gene prediction

Gene prediction and HMM Computational Genomics 2005/6 Lecture 9b

Lecture 22 Word Similarity

Alarm-based prediction:

Improving gene expression similarity measurement using pathway-based analytic dimension

Genome Analysis & Gene Prediction

C omputational ncRNA gene finding (& nc RNA structure prediction)