'Motif finding' presentation slideshows

Motif Finding

Motif Finding. Kun-Pin Wu ( ??? ) Institute of Biomedical Informatics National Yang Ming University 2009/06/06. Finding Regulatory Motifs in DNA Sequences. Random Sample.

1.22k views • 101 slides

CS5263 Bioinformatics

CS5263 Bioinformatics. Lecture 18 Motif finding. What is a (biological) motif?. A motif is a recurring fragment, theme or pattern Sequence motif : a sequence pattern of nucleotides in a DNA sequence or amino acids in a protein

1.14k views • 92 slides

Randomized Algorithms and Motif Finding

Randomized Algorithms and Motif Finding. Outline. Randomized QuickSort Randomized Algorithms Greedy Profile Motif Search Gibbs Sampler Random Projections. Randomized Algorithms. Randomized algorithms make (pseudo) random rather than deterministic decisions.

1.25k views • 85 slides

Randomized Algorithms and Motif Finding

Randomized Algorithms and Motif Finding. Outline. Randomized QuickSort Randomized Algorithms Greedy Profile Motif Search Gibbs Sampler Random Projections. Section 1: Randomized QuickSort. Randomized Algorithms. Randomized Algorithm : Makes random rather than deterministic decisions.

1.06k views • 76 slides

Transcription Regulation Transcription Factor Motif Finding

Transcription Regulation Transcription Factor Motif Finding. Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520. Outline. Biology of transcription regulation and challenges of computational motif finding Scan for known TF motif sites TRASFAC and JASPAR, Sequence Logo De novo method

989 views • 75 slides

Comparative genomics to identify DNA binding motifs

Comparative genomics to identify DNA binding motifs. Saurabh Sinha Dept. of Computer Science University of Illinois, Urbana-Champaign. Outline. Binding sites and motifs The motif finding problem in one species Comparative genomics and alignment

851 views • 70 slides

Discovering gapped binding sites

662 views • 55 slides

CS5263 Bioinformatics

CS5263 Bioinformatics. Lecture 11 Motif finding. HW2 2(C). Click to find out K and lambda. What is a (biological) motif?. A motif is a recurring fragment, theme or pattern Sequence motif : a sequence pattern of nucleotides in a DNA sequence or amino acids in a protein

726 views • 54 slides

Motif Finding

Motif Finding. Yueyi Irene Liu CS374 Lecture Oct. 17, 2002. Outline. Background biology Motif-finding methods Word enumeration Gibbs sampling Random projection Phylogenetic footprinting Reducer. Regulation of Gene Expression. Chromatin structure Transcription initiation

719 views • 52 slides

Detection of Spaced Motifs using Submotif Pattern Mining

Detection of Spaced Motifs using Submotif Pattern Mining. S.M. Yiu Department of Computer Science The University of Hong Kong. Joint work with Ken Sung (Genome Institute of Singapore and NUS) Edward Wijaya, Rajaraman Kanagasabai (Institute for Infocomm Research). Outline.

584 views • 50 slides

CS5263 Bioinformatics

CS5263 Bioinformatics. Lecture 9: Motif finding Biological & Statistical background. Roadmap. Review of last lecture Intro to probability and statistics Intro to motif finding problems Biological background. Multiple Sequence Alignment. Scoring functions. Ideally:

533 views • 43 slides

Motif finding

501 views • 35 slides

Outline

Outline. More exhaustive search algorithms Today: Motif finding regulatory motifs and profiles the motif finding problem brute force motif finding search trees and branch-and-bound motif search the median problem finding the median by branch-and-bound. Transcription Factors and Motifs.

498 views • 35 slides

Bioinformatics

Bioinformatics. Motif Detection Revised 27/10/06. Overview. Introduction Multiple Alignments Multiple alignment based on HMM Motif Finding Motif representation Algorithm Search Space Word counting methods Probabilistic methods Profile Searches Introduction Exercises.

458 views • 34 slides

Gene Regulation and Microarrays

Gene Regulation and Microarrays. Finding Regulatory Motifs. Given a collection of genes with common expression, Find the TF-binding motif in common. Characteristics of Regulatory Motifs. Tiny Highly Variable ~Constant Size Because a constant-size transcription factor binds

391 views • 30 slides

Exhaustive search

726 views • 26 slides

Gibbs sampling for motif finding

Gibbs sampling for motif finding. Yves Moreau. Overview. Markov Chain Monte Carlo Gibbs sampling Motif finding in cis -regulatory DNA Biclustering microarray data. Markov Chain Monte-Carlo. Markov chain with transition matrix T. A C G T

466 views • 24 slides

Dot Plots For Time Series Analysis

Dot Plots For Time Series Analysis. Dragomir Yankov, Eamonn Keogh, Stefano Lonardi Dept. of Computer Science & Eng. University of California Riverside Ada Waichee Fu Dept. of Computer Science & Eng. The Chinese University of Hong Kong. Sequence analysis with dot plots.

299 views • 19 slides

Motif finding methods and algorithms

Motif finding methods and algorithms. Given a set of n promoters of n coregulated genes, find a motif common to the promoters. Both the PWM and the motif sequences are unknown. Common methods: 1 . Enumeration: Simplest case: look at the frequency of all n-mers

410 views • 17 slides

Accelerating HMMER Search on GPUs using Hybrid Task and Data Parallelism

Accelerating HMMER Search on GPUs using Hybrid Task and Data Parallelism. Narayan Ganesan 1 , Roger Chamberlain 2 , Jeremy Buhler 2 and Michela Taufer 1 Computer and Info. Sciences Dept, University of Delaware. 1 Computer Science and Engineering, Washington University in St. Louis 2.

242 views • 14 slides