Protein Sequence Analysis - Overview -

Size: px
Start display at page:

Download "Protein Sequence Analysis - Overview -"

Transcription

1 Protein Sequence Analysis - Overview - UDEL Workshop Raja Mazumder Research Associate Professor, Department of Biochemistry and Molecular Biology Georgetown University Medical Center

2 Topics Why do protein sequence analysis? Searching sequence databases (similarity search) Post-processing search results Protein classification & function prediction. Detecting remote homologs Multiple sequence alignment and Phylogenetic analysis

3 Protein bioinformatics: protein sequence analysis Helps characterize protein sequences in silico and allows prediction of protein structure and function Statistically significant BLAST hits usually signifies sequence homology Homologous sequences may or may not have the same function but would always (very few exceptions) have the same structural fold Protein sequence analysis allows protein classification

4 Comparative protein sequence analysis and evolution Patterns of conservation in sequences allows us to determine which residues are under selective constraint (and thus likely important for protein function) Comparative analysis of proteins is more sensitive than comparing DNA Homologous proteins have a common ancestor Different proteins evolve at different rates Protein classification systems based on evolution: PIRSF and COG

5 Comparing proteins Amino acid sequence of protein generated from proteomics experiment e.g. protein fragment DTIKDLLPNVCAFPMEKGPCQTYMTRWFFNFETGECELFAYGGCGGNSNNFLRKEKCEKFCKFT Amino-acids of two sequences can be aligned and we can easily count the number of identical residues (or use an index of similarity) as a measure of relatedness. Protein structures can be compared by superimposition

6 Protein sequence alignment Pairwise alignment a b a c d a b _ c d Multiple sequence alignment provides more information a b a c d a b _ c d x b a c e MSA difficult to do for distantly related proteins

7 Protein sequence analysis overview Protein databases PIR (pir.georgetown.edu) and UniProt (www.uniprot.org) Searching databases Peptide search, BLAST search, Text search Information retrieval and analysis Protein records at UniProt and PIR Multiple sequence alignment Secondary structure prediction Homology modeling

8 Query Sequence Unknown sequence is Q9I7I7 BLAST Q9I7I7 against the UniProt Knowledgebase (http://www.uniprot.org/search/blast.shtml) Analyze results

9 BLAST results

10 SIR2_HUMAN protein record

11 Are Q9I7I7 and SIR2_HUMAN homologs? Check BLAST results Check pairwise alignment

12 Protein structure prediction Programs can predict secondary structure information with 70% accuracy Homology modeling - prediction of target structure from closely related template structure

13 Secondary structure prediction

14 Secondary structure prediction results

15 Sir2 structure

16 Homology modeling

17 Homology model of Q9I7I7 Blue - excellent Green - so so Red - not good Yellow - beta sheet Red - alpha helix Grey - loop

18 Sequence features: SIR2_HUMAN

19 Multiple sequence alignment

20 Multiple sequence alignment Q9I7I7, Q82QG9, SIR2_HUMAN

21 Identifying Remote Homologs

22 Function prediction

23 Function prediction

24 Molecular Phylogenetics and Evolution Overview History of phylogenetics Sequence analysis and classification Methods in phylogenetic analysis

25 Phylogenetics Field of biology that studies the evolutionary relationships between organisms, proteins or genes that share a common ancestor Phylogenetics includes the discovery (estimation) of these relationships, and the study of the causes behind this pattern Phylogenetics is related taxonomy

26 Tree of Life Aristotle (384 BC 322 BC), classified all living organisms as either a plant or an animal. Whittaker (1969), summarized the "Five Kingdoms" of life: animals, plants, fungi, protists ("protozoa"), and monera (bacteria). R. H. Whittaker, Science 163, 150 (1969) Zuckerkandl et al. (1965) forwarded the concept that sequences could be used to relate organisms. E. Zuckerkandl et al. Biol. 8, 357 (1965). Woese (1990) proposed "urkingdoms" or "domains": Eucarya (eukaryotes), Bacteria (initially called eubacteria), and Archaea (initially called archaebacteria). Woese et al.proc. Natl. Acad. Sci. U.S.A. 87, 4576 (1990). Norman R. Pace Science Vol

27 History of Phylogenetics Charles Darwin Author of The Origin of Species Ernst Haeckel Mapped a genealogical tree relating all animal life. Romanes's 1892 copy of Ernst Haeckel's allegedly fraudulent embryo drawings.

28 Monophyly, Paraphyly & Polyphyly Phylogenetics Wikipedia

29 Molecular Phylogenetics Morphological or organismal character evolution not as consistent compared to molecular evolution Can be used to study any organism Rates of evolution can be studied in greater detail Abundant data available

30 Evolutionary Change in DNA Several models have been proposed to study the mechanisms of DNA evolution Jukes and Cantor s One- Parameter Model assumes no bias in the direction of change so the substitution occur randomly among four types of nucleotides. Kimura s Two-Parameter model transitions are generally more frequent than transversions. The rate of transitional substitution is different than the rate of transversional substitution Rate of change is dependent upon the rate of substitution and pattern of substitution A C T G A > C > T A C > G G T > A A A > C > T C G C Ancestral sequence A C T G A A C G T A A C G C A C > A T G A A C > A G T > A A A > T C G C > T > C Sequence 1 Sequence 2 Single substitution Multiple substitution Coincidental substitution Parallel substitution Convergent substitution Back substitution From Li and Graur 1991

31 Evolutionary Change in Protein Synonymous and nonsynonymous substitutions: Substitutions that result in amino acid replacements are said to be nonsynonymous while substitutions that do not cause an amino acid replacement are said to be synonymous substitutions Changes within the same amino acid classes. Example, hydrophobic, charged, etc.

32 Tutorial Retrieve 1FSI (PDB id) sequence and related sequences from UniProtKB using BLAST Align all the sequences in Clustal (desktop version) Generate tree (using Clustal) View tree (http://www.phylowidget.org/;

33 Representation Of Phylogeny The evolutionary relationship between two proteins can be represented in the form of a tree A phylogeny is a bifurcating tree with nodes and branches and a root (represents the common ancestor) clade Branch Protein 1a Node Root Protein 1b Protein 1c Protein 1d Homologous proteins

34 Terminology Clade A monophyletic taxon Taxon any named group of organisms; not necessarily a clade Branches branches connect nodes Nodes any bifurcating branch point

35 Common Phylogenetic Tree Layout rectangular cladogram slanted cladogram Phylogram (branch lengths proportional to distance) Radial 11

36 Rooted vs. Unrooted Phylogenies R unrooted rooted only relationships not the evolutionary path root (R) is the common ancestor

37 How to Construct A Phylogenetic Tree Construct a multiple sequence alignment Determine the substitution model Build tree Evaluate tree

38 Bootstrapping Bootstrapping is a resampling tree evaluation method A number associated with a particular branch in the tree that gives the proportion of bootstrap replicates that support the monophyly of the clade Two-step process generation of many new data sets from the original set and then the computation of a number that tells how often a particular branch appears in the tree

39 Distance - Neighbor-joining Method NJ algorithm commonly is applied with distance tree building The fully resolved tree is decomposed from a fully unresolved star tree by inserting branches between a pair of closest neighbors and the remaining terminals in the tree. The process is repeated. Rapid method.

40 Function Prediction From Evolutionary Classification Example PFK: Phosphofructokinase classification revealed that major functional specialization can occur as a result not only of major sequence changes but also by mutation of a single amino-acid residue. Families E. coli (P06998) Gly105 Gly125 Classification tree ATP_PFK_DR0635 ATP_PFK_euk PPi_PFK_PfpB PPi_PFK_TM0289 PPi_PFK_TP0108 PPi_PFK_SMc01852 ATP-PFK: Gly105 + Gly125 PPi-PFK: Gly/Asp105 + Lys125 PFK_XF0274

41 Contact Myself- UniProt- PIR-

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

Introduction to Phylogenetic Analysis

Introduction to Phylogenetic Analysis Subjects of this lecture Introduction to Phylogenetic nalysis Irit Orr 1 Introducing some of the terminology of phylogenetics. 2 Introducing some of the most commonly used methods for phylogenetic analysis.

More information

How to Build a Phylogenetic Tree

How to Build a Phylogenetic Tree How to Build a Phylogenetic Tree Phylogenetics tree is a structure in which species are arranged on branches that link them according to their relationship and/or evolutionary descent. A typical rooted

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

Introduction to Bioinformatics AS 250.265 Laboratory Assignment 6

Introduction to Bioinformatics AS 250.265 Laboratory Assignment 6 Introduction to Bioinformatics AS 250.265 Laboratory Assignment 6 In the last lab, you learned how to perform basic multiple sequence alignments. While useful in themselves for determining conserved residues

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

Phylogenetic Trees Made Easy

Phylogenetic Trees Made Easy Phylogenetic Trees Made Easy A How-To Manual Fourth Edition Barry G. Hall University of Rochester, Emeritus and Bellingham Research Institute Sinauer Associates, Inc. Publishers Sunderland, Massachusetts

More information

INTRODUCTION: Topic I: RIBOSOMAL RNA

INTRODUCTION: Topic I: RIBOSOMAL RNA INTRODUCTION: The rrna gene is the most conserved (least variable) DNA in all cells. Portions of the rdna sequence from distantly related organisms are remarkably similar. This means that sequences from

More information

Sequence Analysis 15: lecture 5. Substitution matrices Multiple sequence alignment

Sequence Analysis 15: lecture 5. Substitution matrices Multiple sequence alignment Sequence Analysis 15: lecture 5 Substitution matrices Multiple sequence alignment A teacher's dilemma To understand... Multiple sequence alignment Substitution matrices Phylogenetic trees You first need

More information

Core Bioinformatics. Degree Type Year Semester. 4313473 Bioinformàtica/Bioinformatics OB 0 1

Core Bioinformatics. Degree Type Year Semester. 4313473 Bioinformàtica/Bioinformatics OB 0 1 Core Bioinformatics 2014/2015 Code: 42397 ECTS Credits: 12 Degree Type Year Semester 4313473 Bioinformàtica/Bioinformatics OB 0 1 Contact Name: Sònia Casillas Viladerrams Email: Sonia.Casillas@uab.cat

More information

The Central Dogma of Molecular Biology

The Central Dogma of Molecular Biology Vierstraete Andy (version 1.01) 1/02/2000 -Page 1 - The Central Dogma of Molecular Biology Figure 1 : The Central Dogma of molecular biology. DNA contains the complete genetic information that defines

More information

Three Domains of Life

Three Domains of Life Image from Scientific American blog Three Domains of Life http://www.buzzle.com/articles/three-domains-of-life.html The three-domain system, which classifies life on the planet into three different domains

More information

I. Use BLAST to Find DNA Sequences in Databases (Electronic PCR)

I. Use BLAST to Find DNA Sequences in Databases (Electronic PCR) Using DNA Barcodes to Identify and Classify Living Things: Bioinformatics I. Use BLAST to Find DNA Sequences in Databases (Electronic PCR) 1. Perform a BLAST search as follows: a) Do an Internet search

More information

Table of Contents. Chapter 1 Read Me First! 1. Chapter 2 Tutorial: Estimate a Tree 11

Table of Contents. Chapter 1 Read Me First! 1. Chapter 2 Tutorial: Estimate a Tree 11 Table of Contents Chapter 1 Read Me First! 1 New and Improved Software 2 Just What Is a Phylogenetic Tree? 3 Estimating Phylogenetic Trees: The Basics 4 Beyond the Basics 5 Learn More about the Principles

More information

LAB 21 Using Bioinformatics to Investigate Evolutionary Relationships; Have a BLAST!

LAB 21 Using Bioinformatics to Investigate Evolutionary Relationships; Have a BLAST! LAB 21 Using Bioinformatics to Investigate Evolutionary Relationships; Have a BLAST! Introduction: Between 1990-2003, scientists working on an international research project known as the Human Genome Project,

More information

Biology Performance Level Descriptors

Biology Performance Level Descriptors Limited A student performing at the Limited Level demonstrates a minimal command of Ohio s Learning Standards for Biology. A student at this level has an emerging ability to describe genetic patterns of

More information

NSilico Life Science Introductory Bioinformatics Course

NSilico Life Science Introductory Bioinformatics Course NSilico Life Science Introductory Bioinformatics Course INTRODUCTORY BIOINFORMATICS COURSE A public course delivered over three days on the fundamentals of bioinformatics and illustrated with lectures,

More information

A guided tutorial and Jalview clinic

A guided tutorial and Jalview clinic A guided tutorial and Jalview clinic Jim Procter Barton Group, College of Life Sciences University of Dundee j.procter@dundee.ac.uk FASTA GFF Bioinformatics data is not fun to read.. PDB Newick CSV Alignment

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

Linear Sequence Analysis. 3-D Structure Analysis

Linear Sequence Analysis. 3-D Structure Analysis Linear Sequence Analysis What can you learn from a (single) protein sequence? Calculate it s physical properties Molecular weight (MW), isoelectric point (pi), amino acid content, hydropathy (hydrophilic

More information

Likelihood Ratio Tests for Detecting Positive Selection and Application to Primate Lysozyme Evolution

Likelihood Ratio Tests for Detecting Positive Selection and Application to Primate Lysozyme Evolution Likelihood Ratio Tests for Detecting Positive Selection and Application to Primate Lysozyme Evolution Ziheng Yang Department of Biology, University College, London An excess of nonsynonymous substitutions

More information

Algorithms in Computational Biology (236522) spring 2007 Lecture #1

Algorithms in Computational Biology (236522) spring 2007 Lecture #1 Algorithms in Computational Biology (236522) spring 2007 Lecture #1 Lecturer: Shlomo Moran, Taub 639, tel 4363 Office hours: Tuesday 11:00-12:00/by appointment TA: Ilan Gronau, Taub 700, tel 4894 Office

More information

PHYLOGENETIC ANALYSIS

PHYLOGENETIC ANALYSIS Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition Andreas D. Baxevanis, B.F. Francis Ouellette Copyright 2001 John Wiley & Sons, Inc. ISBNs: 0-471-38390-2 (Hardback);

More information

Visualization of Phylogenetic Trees and Metadata

Visualization of Phylogenetic Trees and Metadata Visualization of Phylogenetic Trees and Metadata November 27, 2015 Sample to Insight CLC bio, a QIAGEN Company Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.clcbio.com support-clcbio@qiagen.com

More information

Guide for Bioinformatics Project Module 3

Guide for Bioinformatics Project Module 3 Structure- Based Evidence and Multiple Sequence Alignment In this module we will revisit some topics we started to look at while performing our BLAST search and looking at the CDD database in the first

More information

Maximum-Likelihood Estimation of Phylogeny from DNA Sequences When Substitution Rates Differ over Sites1

Maximum-Likelihood Estimation of Phylogeny from DNA Sequences When Substitution Rates Differ over Sites1 Maximum-Likelihood Estimation of Phylogeny from DNA Sequences When Substitution Rates Differ over Sites1 Ziheng Yang Department of Animal Science, Beijing Agricultural University Felsenstein s maximum-likelihood

More information

Biology 164 Laboratory PHYLOGENETIC SYSTEMATICS

Biology 164 Laboratory PHYLOGENETIC SYSTEMATICS Biology 164 Laboratory PHYLOGENETIC SYSTEMATICS Objectives 1. To become familiar with the cladistic approach to reconstruction of phylogenies. 2. To construct a character matrix and phylogeny for a group

More information

Last Universal Common Ancestor

Last Universal Common Ancestor Last Universal Common Ancestor Nothing in Biology Makes Sense Except in the Light of Evolution Theodosius Dobzhansky (1900 1975) Dephney Mathebula Dieter Winkler Hloniphile Sithole INTRODUCTION LUCA Last

More information

Bioinformatics Lab. MODULE 1: Sequence Taxonomy

Bioinformatics Lab. MODULE 1: Sequence Taxonomy Student Activity Sheet Name: Bioinformatics Lab MODULE 1: Sequence Taxonomy Objective: The goal of this module is to introduce you to the number and diversity of nucleotide sequences in the NCBI database.

More information

Systematics - BIO 615

Systematics - BIO 615 Outline - and introduction to phylogenetic inference 1. Pre Lamarck, Pre Darwin Classification without phylogeny 2. Lamarck & Darwin to Hennig (et al.) Classification with phylogeny but without a reproducible

More information

Principles of Evolution - Origin of Species

Principles of Evolution - Origin of Species Theories of Organic Evolution X Multiple Centers of Creation (de Buffon) developed the concept of "centers of creation throughout the world organisms had arisen, which other species had evolved from X

More information

Lab 2 - Illustrating Evolutionary Relationships Between Organisms: Emperor Penguins and Phylogenetic Trees

Lab 2 - Illustrating Evolutionary Relationships Between Organisms: Emperor Penguins and Phylogenetic Trees Biology 18 Spring 2008 Lab 2 - Illustrating Evolutionary Relationships Between Organisms: Emperor Penguins and Phylogenetic Trees Pre-Lab Reference Reading: Review pp. 542-556 and pp. 722-737 in Life by

More information

BIO 3350: ELEMENTS OF BIOINFORMATICS PARTIALLY ONLINE SYLLABUS

BIO 3350: ELEMENTS OF BIOINFORMATICS PARTIALLY ONLINE SYLLABUS BIO 3350: ELEMENTS OF BIOINFORMATICS PARTIALLY ONLINE SYLLABUS NEW YORK CITY COLLEGE OF TECHNOLOGY The City University Of New York School of Arts and Sciences Biological Sciences Department Course title:

More information

SAM Teacher s Guide DNA to Proteins

SAM Teacher s Guide DNA to Proteins SAM Teacher s Guide DNA to Proteins Note: Answers to activity and homework questions are only included in the Teacher Guides available after registering for the SAM activities, and not in this sample version.

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

Pairwise Sequence Alignment

Pairwise Sequence Alignment Pairwise Sequence Alignment carolin.kosiol@vetmeduni.ac.at SS 2013 Outline Pairwise sequence alignment global - Needleman Wunsch Gotoh algorithm local - Smith Waterman algorithm BLAST - heuristics What

More information

Student Guide for Mesquite

Student Guide for Mesquite MESQUITE Student User Guide 1 Student Guide for Mesquite This guide describes how to 1. create a project file, 2. construct phylogenetic trees, and 3. map trait evolution on branches (e.g. morphological

More information

Bio-Informatics Lectures. A Short Introduction

Bio-Informatics Lectures. A Short Introduction Bio-Informatics Lectures A Short Introduction The History of Bioinformatics Sanger Sequencing PCR in presence of fluorescent, chain-terminating dideoxynucleotides Massively Parallel Sequencing Massively

More information

Achievement Level Descriptors for Biology

Achievement Level Descriptors for Biology Achievement Level Descriptors for Biology Georgia Department of Education September 2015 All Rights Reserved Achievement Levels and Achievement Level Descriptors With the implementation of the Georgia

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

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

AP Biology Learning Objective Cards

AP Biology Learning Objective Cards 1.1 The student is able to convert a data set from a table of numbers that reflect a change in the genetic makeup of a population over time and to apply mathematical methods and conceptual understandings

More information

BIOINFORMATICS TUTORIAL

BIOINFORMATICS TUTORIAL Bio 242 BIOINFORMATICS TUTORIAL Bio 242 α Amylase Lab Sequence Sequence Searches: BLAST Sequence Alignment: Clustal Omega 3d Structure & 3d Alignments DO NOT REMOVE FROM LAB. DO NOT WRITE IN THIS DOCUMENT.

More information

Section 3 Comparative Genomics and Phylogenetics

Section 3 Comparative Genomics and Phylogenetics Section 3 Section 3 Comparative enomics and Phylogenetics At the end of this section you should be able to: Describe what is meant by DNA sequencing. Explain what is meant by Bioinformatics and Comparative

More information

KEY CONCEPT Organisms can be classified based on physical similarities. binomial nomenclature

KEY CONCEPT Organisms can be classified based on physical similarities. binomial nomenclature Section 17.1: The Linnaean System of Classification Unit 9 Study Guide KEY CONCEPT Organisms can be classified based on physical similarities. VOCABULARY taxonomy taxon binomial nomenclature genus MAIN

More information

Tutorial. Getting started with Ensembl Module 1 Introduction

Tutorial. Getting started with Ensembl  Module 1 Introduction Tutorial Getting started with Ensembl www.ensembl.org Ensembl provides genes and other annotation such as regulatory regions, conserved base pairs across species, and mrna protein mappings to the genome.

More information

Final Project Report

Final Project Report CPSC545 by Introduction to Data Mining Prof. Martin Schultz & Prof. Mark Gerstein Student Name: Yu Kor Hugo Lam Student ID : 904907866 Due Date : May 7, 2007 Introduction Final Project Report Pseudogenes

More information

Building a phylogenetic tree

Building a phylogenetic tree bioscience explained 134567 Wojciech Grajkowski Szkoła Festiwalu Nauki, ul. Ks. Trojdena 4, 02-109 Warszawa Building a phylogenetic tree Aim This activity shows how phylogenetic trees are constructed using

More information

Taxonomy and Classification

Taxonomy and Classification Taxonomy and Classification Taxonomy = the science of naming and describing species Wisdom begins with calling things by their right names -Chinese Proverb museums contain ~ 2 Billion specimens worldwide

More information

Public Health Laboratory Workforce Development Bioinformatics

Public Health Laboratory Workforce Development Bioinformatics Public Health Laboratory Workforce Development Bioinformatics Templates for Course Development Contents Overview... 1 Going Beyond the Introductory Courses... 1 Course Templates... 3 Template 1: Introduction

More information

Arbres formels et Arbre(s) de la Vie

Arbres formels et Arbre(s) de la Vie Arbres formels et Arbre(s) de la Vie A bit of history and biology Definitions Numbers Topological distances Consensus Random models Algorithms to build trees Basic principles DATA sequence alignment distance

More information

Core Bioinformatics. Titulació Tipus Curs Semestre. 4313473 Bioinformàtica/Bioinformatics OB 0 1

Core Bioinformatics. Titulació Tipus Curs Semestre. 4313473 Bioinformàtica/Bioinformatics OB 0 1 Core Bioinformatics 2014/2015 Codi: 42397 Crèdits: 12 Titulació Tipus Curs Semestre 4313473 Bioinformàtica/Bioinformatics OB 0 1 Professor de contacte Nom: Sònia Casillas Viladerrams Correu electrònic:

More information

17.1. The Tree of Life CHAPTER 17. Organisms can be classified based on physical similarities. Linnaean taxonomy. names.

17.1. The Tree of Life CHAPTER 17. Organisms can be classified based on physical similarities. Linnaean taxonomy. names. SECTION 17.1 THE LINNAEAN SYSTEM OF CLASSIFICATION Study Guide KEY CONCEPT Organisms can be classified based on physical similarities. VOCABULARY taxonomy taxon binomial nomenclature genus MAIN IDEA: Linnaeus

More information

WJEC AS Biology Biodiversity & Classification (2.1 All Organisms are related through their Evolutionary History)

WJEC AS Biology Biodiversity & Classification (2.1 All Organisms are related through their Evolutionary History) Name:.. Set:. Specification Points: WJEC AS Biology Biodiversity & Classification (2.1 All Organisms are related through their Evolutionary History) (a) Biodiversity is the number of different organisms

More information

II. Pathways of Discovery in Microbiology. 1.6 The Historical Roots of Microbiology. Robert Hooke and Early Microscopy

II. Pathways of Discovery in Microbiology. 1.6 The Historical Roots of Microbiology. Robert Hooke and Early Microscopy II. Pathways of Discovery in Microbiology 1.6 The Historical Roots of Microbiology 1.6 The Historical Roots of Microbiology 1.7 Pasteur and the Defeat of Spontaneous Generation 1.8 Koch, Infectious Disease,

More information

ECO-1.1: I can describe the processes that move carbon and nitrogen through ecosystems.

ECO-1.1: I can describe the processes that move carbon and nitrogen through ecosystems. Cycles of Matter ECO-1.1: I can describe the processes that move carbon and nitrogen through ecosystems. ECO-1.2: I can explain how carbon and nitrogen are stored in ecosystems. ECO-1.3: I can describe

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

Mammalian Housekeeping Genes Evolve more Slowly. than Tissue-specific Genes

Mammalian Housekeeping Genes Evolve more Slowly. than Tissue-specific Genes MBE Advance Access published October 31, 2003 Mammalian Housekeeping Genes Evolve more Slowly than Tissue-specific Genes Liqing Zhang and Wen-Hsiung Li Department of Ecology and Evolution, University of

More information

Let s get started. So, what is science?

Let s get started. So, what is science? Let s get started So, what is science? Well Science Science is the observation of phenomena and the theoretical explanation of it. Simply, it is the state of knowing. Biology Biology is the study of life.

More information

Evolution Unit Plan. Stage 1: Identify Desired Results Title: Evolution of Life

Evolution Unit Plan. Stage 1: Identify Desired Results Title: Evolution of Life Evolution Unit Plan Stage 1: Identify Desired Results Title: Evolution of Life Unit Description: Evolution is a topic that is fundamental to the study of Biology, linking areas such as genetics, molecular

More information

Genome Explorer For Comparative Genome Analysis

Genome Explorer For Comparative Genome Analysis Genome Explorer For Comparative Genome Analysis Jenn Conn 1, Jo L. Dicks 1 and Ian N. Roberts 2 Abstract Genome Explorer brings together the tools required to build and compare phylogenies from both sequence

More information

AP Biology Essential Knowledge Student Diagnostic

AP Biology Essential Knowledge Student Diagnostic AP Biology Essential Knowledge Student Diagnostic Background The Essential Knowledge statements provided in the AP Biology Curriculum Framework are scientific claims describing phenomenon occurring in

More information

Core Bioinformatics. Degree Type Year Semester

Core Bioinformatics. Degree Type Year Semester Core Bioinformatics 2015/2016 Code: 42397 ECTS Credits: 12 Degree Type Year Semester 4313473 Bioinformatics OB 0 1 Contact Name: Sònia Casillas Viladerrams Email: Sonia.Casillas@uab.cat Teachers Use of

More information

1 Phylogenetic History: The Evolution of Marine Mammals

1 Phylogenetic History: The Evolution of Marine Mammals 1 Phylogenetic History: The Evolution of Marine Mammals Think for a moment about marine mammals: seals, walruses, dugongs and whales. Seals and walruses are primarily cold-water species that eat mostly

More information

What two Assumptions did Darwin have to arrive at BEFORE he could form his theories of evolution?

What two Assumptions did Darwin have to arrive at BEFORE he could form his theories of evolution? Influences on Darwin s Thinking: What ideas did each of the listed names below contribute to Darwin s thinking about evolution? (very brief) Georges Buffon: Jean Baptiste Lamarck: Charles Lyell: Thomas

More information

Name Class Date. Figure 13 1. 2. Which nucleotide in Figure 13 1 indicates the nucleic acid above is RNA? a. uracil c. cytosine b. guanine d.

Name Class Date. Figure 13 1. 2. Which nucleotide in Figure 13 1 indicates the nucleic acid above is RNA? a. uracil c. cytosine b. guanine d. 13 Multiple Choice RNA and Protein Synthesis Chapter Test A Write the letter that best answers the question or completes the statement on the line provided. 1. Which of the following are found in both

More information

Bayesian Phylogeny and Measures of Branch Support

Bayesian Phylogeny and Measures of Branch Support Bayesian Phylogeny and Measures of Branch Support Bayesian Statistics Imagine we have a bag containing 100 dice of which we know that 90 are fair and 10 are biased. The

More information

Evolution at Two Levels in Humans and Chimpanzees

Evolution at Two Levels in Humans and Chimpanzees Evolution at Two Levels in Humans and Chimpanzees Mary-Claire King and A.C. Wilson What did we know prior to 1975? 1700 s: Linnaeus and others of that time considered Great Apes to be the closest relatives

More information

Performance study of supertree methods

Performance study of supertree methods Q&A How did you become involved in doing research? I applied for an REU (Research for Undergraduates) at KU last summer and worked with Dr. Mark Holder for ten weeks. It was an amazing experience! How

More information

A Step-by-Step Tutorial: Divergence Time Estimation with Approximate Likelihood Calculation Using MCMCTREE in PAML

A Step-by-Step Tutorial: Divergence Time Estimation with Approximate Likelihood Calculation Using MCMCTREE in PAML 9 June 2011 A Step-by-Step Tutorial: Divergence Time Estimation with Approximate Likelihood Calculation Using MCMCTREE in PAML by Jun Inoue, Mario dos Reis, and Ziheng Yang In this tutorial we will analyze

More information

Lab 10 Mitosis. Background. Mitosis. Prokaryotic fission. Prophase During prophase, the chromatin. Eukaryotic cell division

Lab 10 Mitosis. Background. Mitosis. Prokaryotic fission. Prophase During prophase, the chromatin. Eukaryotic cell division Lab 10 Mitosis Background Reproduction means producing a new organism from an existing organism. The new offspring must receive hereditary information and enough cytoplasmic material to maintain its own

More information

16 Protein Synthesis: Transcription and Translation

16 Protein Synthesis: Transcription and Translation 16 Protein Synthesis: Transcription and Translation Ge n e s c a r r y t h e information that, along with environmental factors, determines an organism s traits. How does this work? Although the complete

More information

CD-HIT User s Guide. Last updated: April 5, 2010. http://cd-hit.org http://bioinformatics.org/cd-hit/

CD-HIT User s Guide. Last updated: April 5, 2010. http://cd-hit.org http://bioinformatics.org/cd-hit/ CD-HIT User s Guide Last updated: April 5, 2010 http://cd-hit.org http://bioinformatics.org/cd-hit/ Program developed by Weizhong Li s lab at UCSD http://weizhong-lab.ucsd.edu liwz@sdsc.edu 1. Introduction

More information

Exercise 7: DNA and Protein Synthesis

Exercise 7: DNA and Protein Synthesis Exercise 7: DNA and Protein Synthesis Introduction DNA is the code of life, and it is the blueprint for all living things. DNA is contained in all cells, and it is replicated every time a cell divides.

More information

Worksheet - COMPARATIVE MAPPING 1

Worksheet - COMPARATIVE MAPPING 1 Worksheet - COMPARATIVE MAPPING 1 The arrangement of genes and other DNA markers is compared between species in Comparative genome mapping. As early as 1915, the geneticist J.B.S Haldane reported that

More information

Activity IT S ALL RELATIVES The Role of DNA Evidence in Forensic Investigations

Activity IT S ALL RELATIVES The Role of DNA Evidence in Forensic Investigations Activity IT S ALL RELATIVES The Role of DNA Evidence in Forensic Investigations SCENARIO You have responded, as a result of a call from the police to the Coroner s Office, to the scene of the death of

More information

BIOL 1030 TOPIC 1 LECTURE NOTES Topic 1: Classification and the Diversity of Life (Chapters 25, 26.6)

BIOL 1030 TOPIC 1 LECTURE NOTES Topic 1: Classification and the Diversity of Life (Chapters 25, 26.6) Topic 1: Classification and the Diversity of Life (Chapters 25, 26.6) I. Background review (Biology 1020 material) A. Scientific Method 1. observations 2. scientific model explains observations makes testable

More information

Biological Databases and Protein Sequence Analysis

Biological Databases and Protein Sequence Analysis Biological Databases and Protein Sequence Analysis Introduction M. Madan Babu, Center for Biotechnology, Anna University, Chennai 25, India Bioinformatics is the application of Information technology to

More information

1. Over the past century, several scientists around the world have made the following observations:

1. Over the past century, several scientists around the world have made the following observations: Evolution Keystone Review 1. Over the past century, several scientists around the world have made the following observations: New mitochondria and plastids can only be generated by old mitochondria and

More information

Nutrient Assimilation - Taking Up the Right Stuff. Each Fundamental Process of Life

Nutrient Assimilation - Taking Up the Right Stuff. Each Fundamental Process of Life Absorption Ingestion Photosynthesis Each Fundamental Process of Life Unity of Life Universal physical and chemical principles Diversity of Life places design constraints on provides certain opportunities

More information

What next? Computational Biology and Bioinformatics. Finding homologs 2. Finding homologs. 4. Searching for homologs with BLAST

What next? Computational Biology and Bioinformatics. Finding homologs 2. Finding homologs. 4. Searching for homologs with BLAST Computational Biology and Bioinformatics 4. Searching for homologs with BLAST What next? Comparing sequences and searching for homologs Sequence alignment and substitution matrices Searching for sequences

More information

A response to charges of error in Biology by Miller & Levine

A response to charges of error in Biology by Miller & Levine A response to charges of error in Biology by Miller & Levine According to TEA, a citizen disputes two sentences on page 767 of our textbook, Biology, by Miller & Levine. These sentences are: SE 767, par.

More information

Pairwise sequence alignments

Pairwise sequence alignments Pairwise sequence alignments Volker Flegel Vassilios Ioannidis VI - 2004 Page 1 Outline Introduction Definitions Biological context of pairwise alignments Computing of pairwise alignments Some programs

More information

Background Knowledge: Students should understand the structure of DNA and basic genetics.

Background Knowledge: Students should understand the structure of DNA and basic genetics. Biology STANDARD V: Objective 3 Title: Investigating Common Descent Background Knowledge: Students should understand the structure of DNA and basic genetics. Objective: In this activity students will build

More information

Parallel Adaptations to High Temperatures in the Archean Eon

Parallel Adaptations to High Temperatures in the Archean Eon Parallel Adaptations to High Temperatures in the Archean Eon Samuel Blanquart a1 Bastien Boussau b1 Anamaria Necşulea b Nicolas Lartillot a Manolo Gouy b June 9, 2008 a LIRMM, CNRS. b BBE, CNRS, Université

More information

Grade EOC Biology STAAR and STAAR-M Fall 2012 by Objective

Grade EOC Biology STAAR and STAAR-M Fall 2012 by Objective TEKS: (4) The student knows that cells are the basic structures of all living things with specialized parts that perform specific functions, and that viruses are different from cells. Objective: (A) Compare

More information

A branch-and-bound algorithm for the inference of ancestral. amino-acid sequences when the replacement rate varies among

A branch-and-bound algorithm for the inference of ancestral. amino-acid sequences when the replacement rate varies among A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites Tal Pupko 1,*, Itsik Pe er 2, Masami Hasegawa 1, Dan Graur 3, and Nir Friedman

More information

2011.008a-cB. Code assigned:

2011.008a-cB. Code assigned: This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the

More information

PHYML Online: A Web Server for Fast Maximum Likelihood-Based Phylogenetic Inference

PHYML Online: A Web Server for Fast Maximum Likelihood-Based Phylogenetic Inference PHYML Online: A Web Server for Fast Maximum Likelihood-Based Phylogenetic Inference Stephane Guindon, F. Le Thiec, Patrice Duroux, Olivier Gascuel To cite this version: Stephane Guindon, F. Le Thiec, Patrice

More information

AS Biology Unit 2 Key Terms and Definitions. Make sure you use these terms when answering exam questions!

AS Biology Unit 2 Key Terms and Definitions. Make sure you use these terms when answering exam questions! AS Biology Unit 2 Key Terms and Definitions Make sure you use these terms when answering exam questions! Chapter 7 Variation 7.1 Random Sampling Sampling a population to eliminate bias e.g. grid square

More information

Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes

Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, Dec. 1998, p. 1435 1491 Vol. 62, No. 4 1092-2172/98/$04.00 0 Copyright 1998, American Society for Microbiology. All Rights Reserved. Protein Phylogenies and

More information

CHAPTER 1 A VIEW OF LIFE

CHAPTER 1 A VIEW OF LIFE CHAPTER 1 A VIEW OF LIFE 1.1 How to Define Life Living things are called organisms. Organisms are often hard to define because they are so diverse; however, they share many common characteristics: 1. Living

More information

Theory of Evolution. A. the beginning of life B. the evolution of eukaryotes C. the evolution of archaebacteria D. the beginning of terrestrial life

Theory of Evolution. A. the beginning of life B. the evolution of eukaryotes C. the evolution of archaebacteria D. the beginning of terrestrial life Theory of Evolution 1. In 1966, American biologist Lynn Margulis proposed the theory of endosymbiosis, or the idea that mitochondria are the descendents of symbiotic, aerobic eubacteria. What does the

More information

Animal Form and Function. Vertebrate Animals. Kingdom Animalia. A combination of features distinguish the Animalia from all other Kingdoms

Animal Form and Function. Vertebrate Animals. Kingdom Animalia. A combination of features distinguish the Animalia from all other Kingdoms Animal Form and Function Kight Vertebrate Animals Kingdom Animalia A combination of features distinguish the Animalia from all other Kingdoms 1. Eukaryotic cells. 2. Heterotrophic Thought Question: What

More information

Bioinformatics Resources at a Glance

Bioinformatics Resources at a Glance Bioinformatics Resources at a Glance A Note about FASTA Format There are MANY free bioinformatics tools available online. Bioinformaticists have developed a standard format for nucleotide and protein sequences

More information

Phylogenetic Analysis using MapReduce Programming Model

Phylogenetic Analysis using MapReduce Programming Model 2015 IEEE International Parallel and Distributed Processing Symposium Workshops Phylogenetic Analysis using MapReduce Programming Model Siddesh G M, K G Srinivasa*, Ishank Mishra, Abhinav Anurag, Eklavya

More information

Molecular Biology of The Cell - An Introduction

Molecular Biology of The Cell - An Introduction Molecular Biology of The Cell - An Introduction Nguyen Phuong Thao School of Biotechnology International University Contents Three Domain of Life The Cell Eukaryotic Cell Prokaryotic Cell The Genome The

More information

Bioinformatics: Network Analysis

Bioinformatics: Network Analysis Bioinformatics: Network Analysis Molecular Cell Biology: A Brief Review COMP 572 (BIOS 572 / BIOE 564) - Fall 2013 Luay Nakhleh, Rice University 1 The Tree of Life 2 Prokaryotic vs. Eukaryotic Cell Structure

More information

Bioinformatics for Biologists. Protein Structure

Bioinformatics for Biologists. Protein Structure Bioinformatics for Biologists Comparative Protein Analysis: Part III. Protein Structure Prediction and Comparison Robert Latek, PhD Sr. Bioinformatics Scientist Whitehead Institute for Biomedical Research

More information