Metagenomic and metatranscriptomic analysis

Size: px
Start display at page:

Download "Metagenomic and metatranscriptomic analysis"

Transcription

1 Metagenomic and metatranscriptomic analysis Marcelo Falsarella Carazzolle Laboratório de Genômica e Expressão (LGE) Unicamp

2 METAGENOMIC Jo Handelsman (1998) University of Wisconsin-EUA)

3 METAGENÔMICA Marcadores moleculares (16S rrna) Carl Woese Biblioteca de 16S procariotos NGS Acreditava-se que todos os microrganismos eram cultiváveis. Extração do DNA direto do meio ambiente Metagenômica Quem são? O que eles fazem e como fazem?

4 METAGENÔMICA É a análise genômica das comunidades de microrganismos de um determinado ambiente ou habitat. O DNA amostrado é uma mistura de vários microrganismos

5 Meta-approaches

6 Microbial community

7 - Microbial populations - Bacterial 16S Ribosomal RNA - Fungal ITS - Metagenome sequencing - Genome assembly (wide distribution of genome coverage) - Gene prediction (based on ORF finder) - Identification of new enzymes based on conserved domain - Metatranscriptomic sequencing - Transcriptome assembly - Identification of new enzymes - Full-length cdna

8 Phylum level

9 Genus level

10 HP + = hot phenol

11

12

13

14

15

16

17 Microbial diversity - Mitochondrial gene (COX1) for animals - Ribulose 1,5-bisphosphate carboxylase gene (rbcl) for plants - Internal transcribed spacer of the ribosomal DNA (ITS) for fungi - 16S ribosomal RNA for bacteria

18

19

20

21 Ribosomal genes

22 V4 region in 16S DNA barcode for bacteria 254 bp

23 Communicating current research and educational topics and trends in applied microbiology. Formatex, Spain, pp (2007)

24 ITS region universal DNA barcode for fungi ITS length from ~300 to ~1200 bp

25 Ribosomal databases - Greengenes S rrna gene database and alignment - Download: FASTA and ARB file format - Silva - - aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) rrna for all three domains of life (Bacteria, Archaea and Eukarya) - Download: FASTA and ARB file format

26 RNA secondary structural alignment

27 Primers forward Primers reverse

28

29

30 METAGENÔMICA Terragenome - James R. Cole and James M. Tiedje from Michigan State University, David D. Myrold from Oregon State University, Cindy H. Nakatsu, Phillip R. Owens and from Purdue University, George Kowalchuk from Netherlands Institute of Ecology, Christoph Tebbe from Institut für Biodiversität, Braunschweig, 2010

31 METAGENÔMICA Earth Microbiome - Jack A. Gilbert, Folker Meyer and Rick Stevens from Argonne National Laboratory and University of Chicago, Jonathan Eisen (University of California, Davis), Jed Fuhrman (University of Southern California), Janet Jansson (Lawrence Berkley National Laboratory), Rob Knight and Noah Fierer (University of Colorado, Boulder), Mark Bailey (Center for Ecology and Hydrology, UK), George Kowalchuk (Netherlands Institute of Ecology), 2010.

32

33 High throughput sequencing (150) (200)

34 MiSeq atual performance

35 A combination of high throughput sequencing with pairedend reads and barcode methodologies 16S rrna Fungal ITS

36

37

38

39 OTU (operational taxonomic unit) Bioinformatics/blob/master/algorithms/5-sequence-mapping-and-clustering.ipynb?create=1

40 Furthest neighbor clustering

41 Nearest neighbor clustering

42 Centroid clustering

43

44 Rarefaction curve

45

46

47

48

49 HMM BLASTx

50 Samples Taxonomy groups and false discovery rate (FDR).

51 Family level resolution (100bp non overlapping paired-end reads)

52 Genus level =>

53 Metagenomics and metatranscriptomics assembly Grafo de De Bruijn (Kmer = 7) Fonte:

54 Read: ATGGACCAGATGACAC (k=12) => ATGGACCAGATG TGGACCAGATGA GGACCAGATGAC GACCAGATGACA ACCAGATGACAC Dividir todos os reads em palavras de tamanho k (kmers) Contar número de ocorrências de cada k-mer distinto em todo o dataset

55 Grafo de De Bruijn

56

57

58

59

60 Reads per kilobase per million (RPKM)

61 Gene prediction in metagenomic and metatranscriptomic data

62

63 Conceito de ORF (Open Read Frame) Tamanho mínimo das ORFs => ~7 x 10-5 para L=50aa

64

65

66

67 Microbial diversity for enviromental risk assessment -Bacteria => V4 region amplification and sequencing via MiSeq -Fungi => ITS region amplification and sequencing via MiSeq -Barcode (46 samples/run) and paired-end (2x300bp) methodologies => ~U$1.200,00 -Large scale analysis using MOTHUR pipeline and SILVA ribosomal database (16S) -New methodologies for Fungal ITS analysis need to be developed

68

69 The V4 region in 16S ribosomal gene and ITS region in trascribed ribosomal locus are amplified and sequenced using high-throughput sequencing technology producing millions of overlapping paired-end reads. Multiple samples can be sequenced together using multiplexing adapter system.

70

71 Bacterial diversity Fungal diversity

72

73 FIM

Next Generation Sequencing Technologies in Microbial Ecology. Frank Oliver Glöckner

Next Generation Sequencing Technologies in Microbial Ecology. Frank Oliver Glöckner Next Generation Sequencing Technologies in Microbial Ecology Frank Oliver Glöckner 1 Max Planck Institute for Marine Microbiology Investigation of the role, diversity and features of microorganisms Interactions

More information

MoBEDAC -- Integrated data and analysis for the indoor and built environment. Folker Meyer Argonne National Laboratory GSC 13 Shenzhen, China

MoBEDAC -- Integrated data and analysis for the indoor and built environment. Folker Meyer Argonne National Laboratory GSC 13 Shenzhen, China MoBEDAC -- Integrated data and analysis for the indoor and built environment Folker Meyer Argonne National Laboratory GSC 13 Shenzhen, China NGS is causing paradigm shift Environmental clone libraries

More information

A Tutorial in Genetic Sequence Classification Tools and Techniques

A Tutorial in Genetic Sequence Classification Tools and Techniques A Tutorial in Genetic Sequence Classification Tools and Techniques Jake Drew Data Mining CSE 8331 Southern Methodist University jakemdrew@gmail.com www.jakemdrew.com Sequence Characters IUPAC nucleotide

More information

Name: Class: Date: Multiple Choice Identify the choice that best completes the statement or answers the question.

Name: Class: Date: Multiple Choice Identify the choice that best completes the statement or answers the question. Name: Class: Date: Chapter 17 Practice Multiple Choice Identify the choice that best completes the statement or answers the question. 1. The correct order for the levels of Linnaeus's classification system,

More information

NORTH PACIFIC RESEARCH BOARD SEMIANNUAL PROGRESS REPORT

NORTH PACIFIC RESEARCH BOARD SEMIANNUAL PROGRESS REPORT 1. PROJECT INFORMATION NPRB Project Number: 1303 Title: Assessing benthic meiofaunal community structure in the Alaskan Arctic: A high-throughput DNA sequencing approach Subaward period July 1, 2013 Jun

More information

Accelerate genomic breakthroughs in microbiology. Gain deeper insights with powerful bioinformatic tools.

Accelerate genomic breakthroughs in microbiology. Gain deeper insights with powerful bioinformatic tools. Accelerate genomic breakthroughs in microbiology. Gain deeper insights with powerful bioinformatic tools. Empowering microbial genomics. Extensive methods. Expansive possibilities. In microbiome studies

More information

Microbial Oceanomics using High-Throughput DNA Sequencing

Microbial Oceanomics using High-Throughput DNA Sequencing Microbial Oceanomics using High-Throughput DNA Sequencing Ramiro Logares Institute of Marine Sciences, CSIC, Barcelona 9th RES Users'Conference 23 September 2015 Importance of microbes in the sunlit ocean

More information

Name Class Date. binomial nomenclature. MAIN IDEA: Linnaeus developed the scientific naming system still used today.

Name Class Date. binomial nomenclature. MAIN IDEA: Linnaeus developed the scientific naming system still used today. Section 1: The Linnaean System of Classification 17.1 Reading Guide KEY CONCEPT Organisms can be classified based on physical similarities. VOCABULARY taxonomy taxon binomial nomenclature genus MAIN IDEA:

More information

Shouguo Gao Ph. D Department of Physics and Comprehensive Diabetes Center

Shouguo Gao Ph. D Department of Physics and Comprehensive Diabetes Center Computational Challenges in Storage, Analysis and Interpretation of Next-Generation Sequencing Data Shouguo Gao Ph. D Department of Physics and Comprehensive Diabetes Center Next Generation Sequencing

More information

Reliable PCR Components for Molecular Diagnostic Assays

Reliable PCR Components for Molecular Diagnostic Assays Reliable PCR Components for Molecular Diagnostic Assays Terri McDonnell, MBA, PMP Senior Program Manager, Molecular Diagnostics March 2014 In this webinar we will: Discuss requirements for amplification

More information

DNA Barcoding in Plants: Biodiversity Identification and Discovery

DNA Barcoding in Plants: Biodiversity Identification and Discovery DNA Barcoding in Plants: Biodiversity Identification and Discovery University of Sao Paulo December 2009 W. John Kress Department of Botany National Museum of Natural History Smithsonian Institution New

More information

Richmond, VA. Richmond, VA. 2 Department of Microbiology and Immunology, Virginia Commonwealth University,

Richmond, VA. Richmond, VA. 2 Department of Microbiology and Immunology, Virginia Commonwealth University, Massive Multi-Omics Microbiome Database (M 3 DB): A Scalable Data Warehouse and Analytics Platform for Microbiome Datasets Shaun W. Norris 1 (norrissw@vcu.edu) Steven P. Bradley 2 (bradleysp@vcu.edu) Hardik

More information

G E N OM I C S S E RV I C ES

G E N OM I C S S E RV I C ES GENOMICS SERVICES THE NEW YORK GENOME CENTER NYGC is an independent non-profit implementing advanced genomic research to improve diagnosis and treatment of serious diseases. capabilities. N E X T- G E

More information

A Primer of Genome Science THIRD

A Primer of Genome Science THIRD A Primer of Genome Science THIRD EDITION GREG GIBSON-SPENCER V. MUSE North Carolina State University Sinauer Associates, Inc. Publishers Sunderland, Massachusetts USA Contents Preface xi 1 Genome Projects:

More information

Protocols. Internal transcribed spacer region (ITS) region. Niklaus J. Grünwald, Frank N. Martin, and Meg M. Larsen (2013)

Protocols. Internal transcribed spacer region (ITS) region. Niklaus J. Grünwald, Frank N. Martin, and Meg M. Larsen (2013) Protocols Internal transcribed spacer region (ITS) region Niklaus J. Grünwald, Frank N. Martin, and Meg M. Larsen (2013) The nuclear ribosomal RNA (rrna) genes (small subunit, large subunit and 5.8S) are

More information

Frequently Asked Questions Next Generation Sequencing

Frequently Asked Questions Next Generation Sequencing Frequently Asked Questions Next Generation Sequencing Import These Frequently Asked Questions for Next Generation Sequencing are some of the more common questions our customers ask. Questions are divided

More information

Tutorial for Windows and Macintosh. Preparing Your Data for NGS Alignment

Tutorial for Windows and Macintosh. Preparing Your Data for NGS Alignment Tutorial for Windows and Macintosh Preparing Your Data for NGS Alignment 2015 Gene Codes Corporation Gene Codes Corporation 775 Technology Drive, Ann Arbor, MI 48108 USA 1.800.497.4939 (USA) 1.734.769.7249

More information

Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS)

Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS) Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS) A typical RNA Seq experiment Library construction Protocol variations Fragmentation methods RNA: nebulization,

More information

Data Analysis for Ion Torrent Sequencing

Data Analysis for Ion Torrent Sequencing IFU022 v140202 Research Use Only Instructions For Use Part III Data Analysis for Ion Torrent Sequencing MANUFACTURER: Multiplicom N.V. Galileilaan 18 2845 Niel Belgium Revision date: August 21, 2014 Page

More information

Computational Genomics. Next generation sequencing (NGS)

Computational Genomics. Next generation sequencing (NGS) Computational Genomics Next generation sequencing (NGS) Sequencing technology defies Moore s law Nature Methods 2011 Log 10 (price) Sequencing the Human Genome 2001: Human Genome Project 2.7G$, 11 years

More information

Data Processing of Nextera Mate Pair Reads on Illumina Sequencing Platforms

Data Processing of Nextera Mate Pair Reads on Illumina Sequencing Platforms Data Processing of Nextera Mate Pair Reads on Illumina Sequencing Platforms Introduction Mate pair sequencing enables the generation of libraries with insert sizes in the range of several kilobases (Kb).

More information

Standards, Guidelines and Best Practices for RNA-Seq V1.0 (June 2011) The ENCODE Consortium

Standards, Guidelines and Best Practices for RNA-Seq V1.0 (June 2011) The ENCODE Consortium Standards, Guidelines and Best Practices for RNA-Seq V1.0 (June 2011) The ENCODE Consortium I. Introduction: Sequence based assays of transcriptomes (RNA-seq) are in wide use because of their favorable

More information

restriction enzymes 350 Home R. Ward: Spring 2001

restriction enzymes 350 Home R. Ward: Spring 2001 restriction enzymes 350 Home Restriction Enzymes (endonucleases): molecular scissors that cut DNA Properties of widely used Type II restriction enzymes: recognize a single sequence of bases in dsdna, usually

More information

Tribuna Académica. Overview of Metagenomics for Marine Biodiversity Research 1. Barton E. Slatko* Metagenomics defined

Tribuna Académica. Overview of Metagenomics for Marine Biodiversity Research 1. Barton E. Slatko* Metagenomics defined Tribuna Académica 117 Overview of Metagenomics for Marine Biodiversity Research 1 Barton E. Slatko* We are in the midst of the fastest growing revolution in molecular biology, perhaps in all of life science,

More information

Molecular typing of VTEC: from PFGE to NGS-based phylogeny

Molecular typing of VTEC: from PFGE to NGS-based phylogeny Molecular typing of VTEC: from PFGE to NGS-based phylogeny Valeria Michelacci 10th Annual Workshop of the National Reference Laboratories for E. coli in the EU Rome, November 5 th 2015 Molecular typing

More information

NCBI resources III: GEO and ftp site. Yanbin Yin Spring 2013

NCBI resources III: GEO and ftp site. Yanbin Yin Spring 2013 NCBI resources III: GEO and ftp site Yanbin Yin Spring 2013 1 Homework assignment 2 Search colon cancer at GEO and find a data Series and perform a GEO2R analysis Write a report (in word or ppt) to include

More information

Sequence Formats and Sequence Database Searches. Gloria Rendon SC11 Education June, 2011

Sequence Formats and Sequence Database Searches. Gloria Rendon SC11 Education June, 2011 Sequence Formats and Sequence Database Searches Gloria Rendon SC11 Education June, 2011 Sequence A is the primary structure of a biological molecule. It is a chain of residues that form a precise linear

More information

New Technologies for Sensitive, Low-Input RNA-Seq. Clontech Laboratories, Inc.

New Technologies for Sensitive, Low-Input RNA-Seq. Clontech Laboratories, Inc. New Technologies for Sensitive, Low-Input RNA-Seq Clontech Laboratories, Inc. Outline Introduction Single-Cell-Capable mrna-seq Using SMART Technology SMARTer Ultra Low RNA Kit for the Fluidigm C 1 System

More information

An introduction to bioinformatic tools for population genomic and metagenetic data analysis, 2.5 higher education credits Third Cycle

An introduction to bioinformatic tools for population genomic and metagenetic data analysis, 2.5 higher education credits Third Cycle An introduction to bioinformatic tools for population genomic and metagenetic data analysis, 2.5 higher education credits Third Cycle Faculty of Science; Department of Marine Sciences The Swedish Royal

More information

Microbiology Laboratory: MOLECULAR IDENTIFICATION OF UNKNOWN BACTERIA

Microbiology Laboratory: MOLECULAR IDENTIFICATION OF UNKNOWN BACTERIA Microbiology Laboratory: MOLECULAR IDENTIFICATION OF UNKNOWN BACTERIA Classical Microbiology courses are typically structured to introduce the identification of bacterial species using a series of biochemical

More information

Genetic Analysis. Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis

Genetic Analysis. Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis Genetic Analysis Phenotype analysis: biological-biochemical analysis Behaviour under specific environmental conditions Behaviour of specific genetic configurations Behaviour of progeny in crosses - Genotype

More information

Introduction to NGS data analysis

Introduction to NGS data analysis Introduction to NGS data analysis Jeroen F. J. Laros Leiden Genome Technology Center Department of Human Genetics Center for Human and Clinical Genetics Sequencing Illumina platforms Characteristics: High

More information

SILVAngs - rdna-based microbial community analysis using next-generation sequencing (NGS) data - User Guide

SILVAngs - rdna-based microbial community analysis using next-generation sequencing (NGS) data - User Guide SILVAngs - rdna-based microbial community analysis using next-generation sequencing (NGS) data - User Guide Contact: ngs-contact@arb-silva.de Motivation SILVAngs is a data analysis service for ribosomal

More information

Introduction Bioo Scientific

Introduction Bioo Scientific Next Generation Sequencing Catalog 2014-2015 Introduction Bioo Scientific Bioo Scientific is a global life science company headquartered in Austin, TX, committed to providing innovative products and superior

More information

The world of non-coding RNA. Espen Enerly

The world of non-coding RNA. Espen Enerly The world of non-coding RNA Espen Enerly ncrna in general Different groups Small RNAs Outline mirnas and sirnas Speculations Common for all ncrna Per def.: never translated Not spurious transcripts Always/often

More information

Next Generation Sequencing

Next Generation Sequencing Next Generation Sequencing Technology and applications 10/1/2015 Jeroen Van Houdt - Genomics Core - KU Leuven - UZ Leuven 1 Landmarks in DNA sequencing 1953 Discovery of DNA double helix structure 1977

More information

Structure and Function of DNA

Structure and Function of DNA Structure and Function of DNA DNA and RNA Structure DNA and RNA are nucleic acids. They consist of chemical units called nucleotides. The nucleotides are joined by a sugar-phosphate backbone. The four

More information

PreciseTM Whitepaper

PreciseTM Whitepaper Precise TM Whitepaper Introduction LIMITATIONS OF EXISTING RNA-SEQ METHODS Correctly designed gene expression studies require large numbers of samples, accurate results and low analysis costs. Analysis

More information

AmphoraNet: Taxonomic Composition Analysis of Metagenomic Shotgun Sequencing Data

AmphoraNet: Taxonomic Composition Analysis of Metagenomic Shotgun Sequencing Data Csaba Kerepesi, Dániel Bánky, Vince Grolmusz: AmphoraNet: Taxonomic Composition Analysis of Metagenomic Shotgun Sequencing Data http://pitgroup.org/amphoranet/ PIT Bioinformatics Group, Department of Computer

More information

La capture de la fonction par des approches haut débit

La capture de la fonction par des approches haut débit Colloque Génomique Environnementale LYON 2011 La capture de la fonction par des approches haut débit Pierre PEYRET J. Denonfoux, N. Parisot, E. Dugat-Bony, C. Biderre-Petit, D. Boucher, G. Fonty, E. Peyretaillade

More information

Core Facility Genomics

Core Facility Genomics Core Facility Genomics versatile genome or transcriptome analyses based on quantifiable highthroughput data ascertainment 1 Topics Collaboration with Harald Binder and Clemens Kreutz Project: Microarray

More information

Chapter 9. Biotechnology and Recombinant DNA Biotechnology and Recombinant DNA

Chapter 9. Biotechnology and Recombinant DNA Biotechnology and Recombinant DNA Chapter 9 Biotechnology and Recombinant DNA Biotechnology and Recombinant DNA Q&A Interferons are species specific, so that interferons to be used in humans must be produced in human cells. Can you think

More information

A data management framework for the Fungal Tree of Life

A data management framework for the Fungal Tree of Life Web Accessible Sequence Analysis for Biological Inference A data management framework for the Fungal Tree of Life Kauff F, Cox CJ, Lutzoni F. 2007. WASABI: An automated sequence processing system for multi-gene

More information

Metagenomics revisits the one pathogen/one disease postulates and translate the One Health concept into action

Metagenomics revisits the one pathogen/one disease postulates and translate the One Health concept into action Les Rencontres de L INRA Metagenomics revisits the one pathogen/one disease postulates and translate the One Health concept into action E Albina (CIRAD) / S Guyomard(Institut Pasteur) Guadeloupe The era

More information

Bioinformatics Grid - Enabled Tools For Biologists.

Bioinformatics Grid - Enabled Tools For Biologists. Bioinformatics Grid - Enabled Tools For Biologists. What is Grid-Enabled Tools (GET)? As number of data from the genomics and proteomics experiment increases. Problems arise for the current sequence analysis

More information

An introduction to bioinformatic tools for metagenetic and population genomic data analysis, 2.0 higher education credits

An introduction to bioinformatic tools for metagenetic and population genomic data analysis, 2.0 higher education credits An introduction to bioinformatic tools for metagenetic and population genomic data analysis, 2.0 higher education credits Course period: 3-7 November 2014 Course leaders / Addresses for applications: Pierre

More information

The University is comprised of seven colleges and offers 19. including more than 5000 graduate students.

The University is comprised of seven colleges and offers 19. including more than 5000 graduate students. UNC CHARLOTTE A doctoral, research-intensive university, UNC Charlotte is the largest institution of higher education in the Charlotte region. The University is comprised of seven colleges and offers 19

More information

QBOL, DNA barcodes to identify phytobacteria subjected to EU quarantine regulations

QBOL, DNA barcodes to identify phytobacteria subjected to EU quarantine regulations QBOL, DNA barcodes to identify phytobacteria subjected to EU quarantine regulations Cottyn B., L. Detemmerman, M. Maes COST873 - Annual Meeting 13-15 September 2010 Introduction Financed by 7th Framework

More information

2.3 Identify rrna sequences in DNA

2.3 Identify rrna sequences in DNA 2.3 Identify rrna sequences in DNA For identifying rrna sequences in DNA we will use rnammer, a program that implements an algorithm designed to find rrna sequences in DNA [5]. The program was made by

More information

SMRT Analysis v2.2.0 Overview. 1. SMRT Analysis v2.2.0. 1.1 SMRT Analysis v2.2.0 Overview. Notes:

SMRT Analysis v2.2.0 Overview. 1. SMRT Analysis v2.2.0. 1.1 SMRT Analysis v2.2.0 Overview. Notes: SMRT Analysis v2.2.0 Overview 100 338 400 01 1. SMRT Analysis v2.2.0 1.1 SMRT Analysis v2.2.0 Overview Welcome to Pacific Biosciences' SMRT Analysis v2.2.0 Overview 1.2 Contents This module will introduce

More information

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges Next-Generation DNA Sequencing/Review Microbial community profiling for human microbiome projects: Tools, techniques, and challenges Micah Hamady 1 and Rob Knight 2,3 1 Department of Computer Science,

More information

Genome-scale technologies 2/ Algorithmic and statistical aspects of DNA sequencing What to sequence next? Exciting achievements of the -seq.

Genome-scale technologies 2/ Algorithmic and statistical aspects of DNA sequencing What to sequence next? Exciting achievements of the -seq. Genome-scale technologies 2/ Algorithmic and statistical aspects of DNA sequencing What to sequence next? Exciting achievements of the -seq. Ewa Szczurek University of Warsaw, MIMUW szczurek@mimuw.edu.pl

More information

Molecular and Cell Biology Laboratory (BIOL-UA 223) Instructor: Ignatius Tan Phone: 212-998-8295 Office: 764 Brown Email: ignatius.tan@nyu.

Molecular and Cell Biology Laboratory (BIOL-UA 223) Instructor: Ignatius Tan Phone: 212-998-8295 Office: 764 Brown Email: ignatius.tan@nyu. Molecular and Cell Biology Laboratory (BIOL-UA 223) Instructor: Ignatius Tan Phone: 212-998-8295 Office: 764 Brown Email: ignatius.tan@nyu.edu Course Hours: Section 1: Mon: 12:30-3:15 Section 2: Wed: 12:30-3:15

More information

IIID 14. Biotechnology in Fish Disease Diagnostics: Application of the Polymerase Chain Reaction (PCR)

IIID 14. Biotechnology in Fish Disease Diagnostics: Application of the Polymerase Chain Reaction (PCR) IIID 14. Biotechnology in Fish Disease Diagnostics: Application of the Polymerase Chain Reaction (PCR) Background Infectious diseases caused by pathogenic organisms such as bacteria, viruses, protozoa,

More information

Introduction to Bioinformatics 3. DNA editing and contig assembly

Introduction to Bioinformatics 3. DNA editing and contig assembly Introduction to Bioinformatics 3. DNA editing and contig assembly Benjamin F. Matthews United States Department of Agriculture Soybean Genomics and Improvement Laboratory Beltsville, MD 20708 matthewb@ba.ars.usda.gov

More information

Bioinformatics and its applications

Bioinformatics and its applications Bioinformatics and its applications Alla L Lapidus, Ph.D. SPbAU, SPbSU, St. Petersburg Term Bioinformatics Term Bioinformatics was invented by Paulien Hogeweg (Полина Хогевег) and Ben Hesper in 1970 as

More information

Human Genome and Human Genome Project. Louxin Zhang

Human Genome and Human Genome Project. Louxin Zhang Human Genome and Human Genome Project Louxin Zhang A Primer to Genomics Cells are the fundamental working units of every living systems. DNA is made of 4 nucleotide bases. The DNA sequence is the particular

More information

RETRIEVING SEQUENCE INFORMATION. Nucleotide sequence databases. Database search. Sequence alignment and comparison

RETRIEVING SEQUENCE INFORMATION. Nucleotide sequence databases. Database search. Sequence alignment and comparison RETRIEVING SEQUENCE INFORMATION Nucleotide sequence databases Database search Sequence alignment and comparison Biological sequence databases Originally just a storage place for sequences. Currently the

More information

Nucleic Acid Techniques in Bacterial Systematics

Nucleic Acid Techniques in Bacterial Systematics Nucleic Acid Techniques in Bacterial Systematics Edited by Erko Stackebrandt Department of Microbiology University of Queensland St Lucia, Australia and Michael Goodfellow Department of Microbiology University

More information

The NGS IT notes. George Magklaras PhD RHCE

The NGS IT notes. George Magklaras PhD RHCE The NGS IT notes George Magklaras PhD RHCE Biotechnology Center of Oslo & The Norwegian Center of Molecular Medicine University of Oslo, Norway http://www.biotek.uio.no http://www.ncmm.uio.no http://www.no.embnet.org

More information

Influence of the skin mechanical and microbial properties on hair growth

Influence of the skin mechanical and microbial properties on hair growth Call for Interdisciplinary Projects Sevres 2014 A General Information Project title Influence of the skin mechanical and microbial properties on hair growth Acronym TADDEI: The Ambiguous Dupond and Dupont

More information

14/12/2012. HLA typing - problem #1. Applications for NGS. HLA typing - problem #1 HLA typing - problem #2

14/12/2012. HLA typing - problem #1. Applications for NGS. HLA typing - problem #1 HLA typing - problem #2 www.medical-genetics.de Routine HLA typing by Next Generation Sequencing Kaimo Hirv Center for Human Genetics and Laboratory Medicine Dr. Klein & Dr. Rost Lochhamer Str. 9 D-8 Martinsried Tel: 0800-GENETIK

More information

Introduction to next-generation sequencing data

Introduction to next-generation sequencing data Introduction to next-generation sequencing data David Simpson Centre for Experimental Medicine Queens University Belfast http://www.qub.ac.uk/research-centres/cem/ Outline History of DNA sequencing NGS

More information

ESPRIT-Tree Web Tool User Manual

ESPRIT-Tree Web Tool User Manual ESPRIT-Tree Web Tool User Manual Jin Yao, Wei Zheng and Yijun Sun New York State Center of Excellence in Bioinformatics and Life Sciences The State University of New York at Buffalo, Buffalo, NY 14203

More information

Mir-X mirna First-Strand Synthesis Kit User Manual

Mir-X mirna First-Strand Synthesis Kit User Manual User Manual Mir-X mirna First-Strand Synthesis Kit User Manual United States/Canada 800.662.2566 Asia Pacific +1.650.919.7300 Europe +33.(0)1.3904.6880 Japan +81.(0)77.543.6116 Clontech Laboratories, Inc.

More information

GenBank, Entrez, & FASTA

GenBank, Entrez, & FASTA GenBank, Entrez, & FASTA Nucleotide Sequence Databases First generation GenBank is a representative example started as sort of a museum to preserve knowledge of a sequence from first discovery great repositories,

More information

Cloud BioLinux: Pre-configured and On-demand Bioinformatics Computing for the Genomics Community

Cloud BioLinux: Pre-configured and On-demand Bioinformatics Computing for the Genomics Community Cloud BioLinux: Pre-configured and On-demand Bioinformatics Computing for the Genomics Community Ntinos Krampis Asst. Professor J. Craig Venter Institute kkrampis@jcvi.org http://www.jcvi.org/cms/about/bios/kkrampis/

More information

Daniel H. Huson. January 21, 2016. Contents 1. 1 Introduction 3. 2 Getting Started 5. 4 Licensing 6. 5 Program Overview 7. 7 Taxonomic Binning 9

Daniel H. Huson. January 21, 2016. Contents 1. 1 Introduction 3. 2 Getting Started 5. 4 Licensing 6. 5 Program Overview 7. 7 Taxonomic Binning 9 User Manual for MEGAN V5.11.3 Daniel H. Huson January 21, 2016 Contents Contents 1 1 Introduction 3 2 Getting Started 5 3 Obtaining and Installing the Program 5 4 Licensing 6 5 Program Overview 7 6 Importing,

More information

Molecular diagnostic: from research to application

Molecular diagnostic: from research to application FEM2 Ambiente S.r.l. spin-off dell' UNIVERSITA' DEGLI STUDI DI MILANO-BICOCCA Molecular diagnostic: from research to application Emanuele Ferri & Andrea Galimberti Le biotecnologie nel mondo della criminologia

More information

RNA-Seq Tutorial 1. John Garbe Research Informatics Support Systems, MSI March 19, 2012

RNA-Seq Tutorial 1. John Garbe Research Informatics Support Systems, MSI March 19, 2012 RNA-Seq Tutorial 1 John Garbe Research Informatics Support Systems, MSI March 19, 2012 Tutorial 1 RNA-Seq Tutorials RNA-Seq experiment design and analysis Instruction on individual software will be provided

More information

Deep Sequencing Data Analysis

Deep Sequencing Data Analysis Deep Sequencing Data Analysis Ross Whetten Professor Forestry & Environmental Resources Background Who am I, and why am I teaching this topic? I am not an expert in bioinformatics I started as a biologist

More information

Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources

Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources 1 of 8 11/7/2004 11:00 AM National Center for Biotechnology Information About NCBI NCBI at a Glance A Science Primer Human Genome Resources Model Organisms Guide Outreach and Education Databases and Tools

More information

Rules and Format for Taxonomic Nucleotide Sequence Annotation for Fungi: a proposal

Rules and Format for Taxonomic Nucleotide Sequence Annotation for Fungi: a proposal Rules and Format for Taxonomic Nucleotide Sequence Annotation for Fungi: a proposal The need for third-party sequence annotation Taxonomic names attached to nucleotide sequences occasionally need to be

More information

Activity 7.21 Transcription factors

Activity 7.21 Transcription factors Purpose To consolidate understanding of protein synthesis. To explain the role of transcription factors and hormones in switching genes on and off. Play the transcription initiation complex game Regulation

More information

nuts and bolts of DNA sequencing approaches and bioinformatic tools

nuts and bolts of DNA sequencing approaches and bioinformatic tools nuts and bolts of DNA sequencing approaches and bioinformatic tools Dionysios A. Antonopoulos Institute for Genomics and Systems Biology Biosciences Division Argonne National Laboratory August 7, 2012

More information

Description: Molecular Biology Services and DNA Sequencing

Description: Molecular Biology Services and DNA Sequencing Description: Molecular Biology s and DNA Sequencing DNA Sequencing s Single Pass Sequencing Sequence data only, for plasmids or PCR products Plasmid DNA or PCR products Plasmid DNA: 20 100 ng/μl PCR Product:

More information

Lab 2/Phylogenetics/September 16, 2002 1 PHYLOGENETICS

Lab 2/Phylogenetics/September 16, 2002 1 PHYLOGENETICS Lab 2/Phylogenetics/September 16, 2002 1 Read: Tudge Chapter 2 PHYLOGENETICS Objective of the Lab: To understand how DNA and protein sequence information can be used to make comparisons and assess evolutionary

More information

COMPARING DNA SEQUENCES TO DETERMINE EVOLUTIONARY RELATIONSHIPS AMONG MOLLUSKS

COMPARING DNA SEQUENCES TO DETERMINE EVOLUTIONARY RELATIONSHIPS AMONG MOLLUSKS COMPARING DNA SEQUENCES TO DETERMINE EVOLUTIONARY RELATIONSHIPS AMONG MOLLUSKS OVERVIEW In the online activity Biodiversity and Evolutionary Trees: An Activity on Biological Classification, you generated

More information

When you install Mascot, it includes a copy of the Swiss-Prot protein database. However, it is almost certain that you and your colleagues will want

When you install Mascot, it includes a copy of the Swiss-Prot protein database. However, it is almost certain that you and your colleagues will want 1 When you install Mascot, it includes a copy of the Swiss-Prot protein database. However, it is almost certain that you and your colleagues will want to search other databases as well. There are very

More information

A rapid and low-cost method for assessing AD plant health through identification of functional microbial communities

A rapid and low-cost method for assessing AD plant health through identification of functional microbial communities Feasibility Report A rapid and low-cost method for assessing AD plant health through identification of functional microbial communities A feasibility report from the Driving Innovation in AD programme

More information

NGS Data Analysis: An Intro to RNA-Seq

NGS Data Analysis: An Intro to RNA-Seq NGS Data Analysis: An Intro to RNA-Seq March 25th, 2014 GST Colloquim: March 25th, 2014 1 / 1 Workshop Design Basics of NGS Sample Prep RNA-Seq Analysis GST Colloquim: March 25th, 2014 2 / 1 Experimental

More information

Overview sequence projects

Overview sequence projects Overview sequence projects Bioassist NGS meeting 15-01-2010 Barbera van Schaik KEBB - Bioinformatics Laboratory b.d.vanschaik@amc.uva.nl NGS at the Academic Medical Center Sequence facility Laboratory

More information

Typing in the NGS era: The way forward!

Typing in the NGS era: The way forward! Typing in the NGS era: The way forward! Valeria Michelacci NGS course, June 2015 Typing from sequence data NGS-derived conventional Multi Locus Sequence Typing (University of Warwick, 7 housekeeping genes)

More information

Ribosomes and Antibiotics.

Ribosomes and Antibiotics. Ribosomes and Antibiotics www.biochemj.org/bj/330/0581/bj3300581.htm Ribosomes as evolutionarily conserved nanomachines required to make proteins Why study ribosome structure? Why study ribosomes from

More information

International CEMarin Omics Workshop: Omics Techniques for the Study of Marine Organisms and Ecosystems

International CEMarin Omics Workshop: Omics Techniques for the Study of Marine Organisms and Ecosystems International CEMarin Omics Workshop: Omics Techniques for the Study of Marine Organisms and Ecosystems Genomics, proteomics and metabolomics, used alone, in combination with each other and/or with more

More information

THE INTERESTING HISTORY OF CELLS STUDENT HANDOUT. There are two basic types of cells, prokaryotic cells and eukaryotic cells.

THE INTERESTING HISTORY OF CELLS STUDENT HANDOUT. There are two basic types of cells, prokaryotic cells and eukaryotic cells. THE INTERESTING HISTORY OF CELLS STUDENT HANDOUT There are two basic types of cells, prokaryotic cells and eukaryotic cells. Figure 1. A PROKARYOTIC CELL The prokaryotes are very small singlecelled organisms

More information

Module 10: Bioinformatics

Module 10: Bioinformatics Module 10: Bioinformatics 1.) Goal: To understand the general approaches for basic in silico (computer) analysis of DNA- and protein sequences. We are going to discuss sequence formatting required prior

More information

Bioinformática BLAST. Blast information guide. Buscas de sequências semelhantes. Search for Homologies BLAST

Bioinformática BLAST. Blast information guide. Buscas de sequências semelhantes. Search for Homologies BLAST BLAST Bioinformática Search for Homologies BLAST BLAST - Basic Local Alignment Search Tool http://blastncbinlmnihgov/blastcgi 1 2 Blast information guide Buscas de sequências semelhantes http://blastncbinlmnihgov/blastcgi?cmd=web&page_type=blastdocs

More information

PLNT2530 Unit 6e DNA Sequencing

PLNT2530 Unit 6e DNA Sequencing PLNT2530 Unit 6e DNA Sequencing Unless otherwise cited or referenced, all content of this presenataion is licensed under the Creative Commons License Attribution Share-Alike 2.5 Canada 1 High-throughput

More information

PAGANTEC: OPENMP PARALLEL ERROR CORRECTION FOR NEXT-GENERATION SEQUENCING DATA

PAGANTEC: OPENMP PARALLEL ERROR CORRECTION FOR NEXT-GENERATION SEQUENCING DATA PAGANTEC: OPENMP PARALLEL ERROR CORRECTION FOR NEXT-GENERATION SEQUENCING DATA Markus Joppich, Tony Bolger, Dirk Schmidl Björn Usadel and Torsten Kuhlen Markus Joppich Lehr- und Forschungseinheit Bioinformatik

More information

Algorithms for Next Generation Sequencing Data Analysis

Algorithms for Next Generation Sequencing Data Analysis UNIVERSITÀ DEGLI STUDI DI MILANO - BICOCCA FACOLTÀ DI SCIENZE MATEMATICHE, FISICHE E NATURALI DIPARTIMENTO DI INFORMATICA, SISTEMISTICA E COMUNICAZIONE DOTTORATO DI RICERCA IN INFORMATICA - CICLO XXV Ph.D.

More information

Genomics for Dummies. Bio informatics and Comparative Genomes Analysis: Jean Michel Claverie 6 18 mai 2013

Genomics for Dummies. Bio informatics and Comparative Genomes Analysis: Jean Michel Claverie 6 18 mai 2013 Genomics for Dummies Bio informatics and Comparative Genomes Analysis: Jean Michel Claverie 6 18 mai 2013 Do I need to know more than just this telephone number? Introduction Try to learn/understand things

More information

4. Why are common names not good to use when classifying organisms? Give an example.

4. Why are common names not good to use when classifying organisms? Give an example. 1. Define taxonomy. Classification of organisms 2. Who was first to classify organisms? Aristotle 3. Explain Aristotle s taxonomy of organisms. Patterns of nature: looked like 4. Why are common names not

More information

IMBB 2013. Genomic DNA purifica8on

IMBB 2013. Genomic DNA purifica8on IMBB 2013 Genomic DNA purifica8on Why purify DNA? The purpose of DNA purifica8on from the cell/8ssue is to ensure it performs well in subsequent downstream applica8ons, e.g. Polymerase Chain Reac8on (PCR),

More information

Data integration for metagenomics: current status and future plans

Data integration for metagenomics: current status and future plans integration for metagenomics: current status and future plans Neil Wipat Computing Science University of Newcastle NERC Microbial Metagenomics Overview metamicrobase Current method of data integration

More information

Cloud BioLinux: Pre-configured and On-demand Bioinformatics Computing for the Genomics Community

Cloud BioLinux: Pre-configured and On-demand Bioinformatics Computing for the Genomics Community Cloud BioLinux: Pre-configured and On-demand Bioinformatics Computing for the Genomics Community Ntinos Krampis Asst. Professor J. Craig Venter Institute kkrampis@jcvi.org http://www.jcvi.org/cms/about/bios/kkrampis/

More information

Removing Sequential Bottlenecks in Analysis of Next-Generation Sequencing Data

Removing Sequential Bottlenecks in Analysis of Next-Generation Sequencing Data Removing Sequential Bottlenecks in Analysis of Next-Generation Sequencing Data Yi Wang, Gagan Agrawal, Gulcin Ozer and Kun Huang The Ohio State University HiCOMB 2014 May 19 th, Phoenix, Arizona 1 Outline

More information

Microbiology. Chapter 1. of Microbiology. Many Diverse Disciplines: Biotechnology Genetic engineering & recombinant.

Microbiology. Chapter 1. of Microbiology. Many Diverse Disciplines: Biotechnology Genetic engineering & recombinant. PowerPoint to accompany The Cowan/Talaro Chapter 1 Microbiology: Microbiology Main Themes of A Systems Approach Topics Scope Importance to Cover: Characteristics of Microbiology History Human of Use Microbiology

More information

BIOL 3200 Spring 2015 DNA Subway and RNA-Seq Data Analysis

BIOL 3200 Spring 2015 DNA Subway and RNA-Seq Data Analysis BIOL 3200 Spring 2015 DNA Subway and RNA-Seq Data Analysis By the end of this lab students should be able to: Describe the uses for each line of the DNA subway program (Red/Yellow/Blue/Green) Describe

More information