PPT-Usage of profile HMMs in Bioinformatics

Using PFAM databases profile HMMs in MATLAB Bioinformatics Toolkit Presentation by Athina Ropodi University of Athens Information Technology in Medicine and Biology outline Introduction. Felzenszwalb Daniel P Huttenlocher Jon M Kleinberg AI Lab MIT Cambridge MA 02139 Computer Science Dept Cornell University Ithaca NY 14853 Abstract In applying Hidden Markov Models to the analysis of massive data streams it is often necessary to us First we saw the finite state automaton. The rigid non-stochastic nature of these structures ultimately limited their usefulness to us as models of DNA. 1. 2. 3. 4. 5. 6. 7. 8. S. e. g. g. g. g. c. g. biomolecular. sequence analysis. Nam-phuong Nguyen. Carl R. Woese Institute for Genomic Biology. University of Illinois at Urbana-Champaign. Human Microbiome. 10 times more bacteria cells than human cells. Provided by WV-INBRE. Mary E. Davis, Ph.D.. Bioinformatics Core Director. Outline. Overview of WV-INBRE. Technology supported. Agilent microarray. Illumina. HiSeq1000 (Next Generation Sequencing). Bioinformatics analysis resources supported. Tandy Warnow. BioE. /CS 598AGB. Profile Hidden Markov Models. Basic tool in sequence analysis. Look more complicated than they really are. Used to model a family of sequences. Can be built from a multiple sequence alignment. Chuong. B. Do. CS262, Winter 2009. Lecture #8. Outline. I’ll cover two different topics today. pair-HMMs. conditional random fields (CRFs). Other resources. For more information on pair-HMMs, see the Durbin et al. book. High-throughput Data Analysis. Literature Study. Data Mining . Functional Genomics Analysis. Vector NTI Advance®. Software. License type. License number. 2008. 2009. 2010. 2011. 2012. 2013. 2014. Galaxy. Jan - June 2015. Consulting researchers on bioinformatics tools, data analysis, data management, . and interpretation of experimental . data.. Analyzing of high. -throughput . sequencing data and conducting . Kevin C. Chen. Rutgers University. joint work with . Jimin. Song (Rutgers/. Palentir. ), . Kamalika. Chaudhuri and . Chicheng. Zhang (UCSD). Human Genome-wide Association Studies. ~12,000 human disease SNPs known . Section 1: Introduction and biological databases.. Section 2: Sequence alignment.. Section 3: Gene and promoter prediction.. Section 4: Molecular phylogenetics.. Section 5: Structural Bioinformatics. Dr. Ronald Moura. ronaldmoura1989@gmail.com. https://www.linkedin.com/in/ronald-moura-660017178. /. Gordon Moore . “The . number of transistors in a dense integrated circuit doubles about every two . Lecture 1 – Introduction . to . Bioinformatics. Petrus Tang, Ph.D. (. 鄧致剛. ). Graduate Institute of Basic Medical Sciences. and. Bioinformatics Center, Chang Gung University. .. petang@mail.cgu.edu.tw. , . B.Sc. Biotech Teaching Assistant. Omdurman Islamic University. Bioinformatics Topics. Informatics. Biology. Operating Systems. Windows. , . Macintosh . both offer an intuitive . GUI . … familiarity . There exist different levels of computational methods for . describing metabolic networks:. - stoichiometry/kinetics of classical biochemical . pathways. (glycolysis, TCA cycle, .... - stoichiometric modelling (.