08/21/2017 BLAST. Multiple Sequence Alignments: Clustal Omega

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "08/21/2017 BLAST. Multiple Sequence Alignments: Clustal Omega"

Transcription

1 BLAST Multiple Sequence Alignments: Clustal Omega What does basic BLAST do (e.g. what is input sequence and how does BLAST look for matches?) Susan Parrish McDaniel College Multiple Sequence Alignments & Building Phylogenetic s Basic BLAST: input query and search database for homologous sequences and see pair-wise matches (query/subject) However, what if you want to specify the sequences to align? 1) Two sequences: NCBI-BLAST- (bl2seq) 2) Three or more sequences: Clustal Omega 3) Building trees from multiple sequence alignments: Clustal Simple Phylogeny Clustal: creating a multiple sequence alignment You SELECT sequences to align to identified conserved nucleotides or amino acids What conserved sequences might you identify in a multiple sequence alignment of DNA sequences? What conserved sequences might you identify in a multiple sequence alignment of amino acid sequences? How could you use multiple sequence alignments to build phylogenetic trees? Consensus Nucleotide Sequences A consensus nucleotide sequence is derived by making a multiple sequence alignment and calculating the most represented nucleotide at each position Provides insight into the functional regions of a given sequence (more important for function = conservation through evolution) Example: If a DNA binding site is necessary to recruit a specific protein, expect that DNA sequence to be conserved during evolution Consensus Nucleotide Sequences: Promoters Determine consensus sequence found in promoter for RNA polymerase recruitment by multiple sequence alignments of regions upstream of genes Closer a promoter is to consensus sequence, stronger the promoter in driving expression of gene (better at recruiting RNA polymerase) Individual promoters usually differ from the consensus at one or more positions 1

2 Prokaryotic -10 & -35 Promoter Consensus Sequence Prokaryotic -10 & -35 Promoter Consensus Sequence The prokaryotic promoter consensus sequence Closer to this sequence, more easily recognized by prokaryotic RNA polymerase Sense A Eukaryotic Consensus Sequence Proteins: Conserved Domains Can find conserved domains in proteins by performing multiple sequence alignments of amino acid sequences If a region of a protein has a particular function that is important (e.g. DNA binding domain/ protein-protein interaction domain/ enzymatic active site) will see conservation of amino acids within that domain Conserved domains tend to fold independently of other parts of protein (therefore structure of domain conserved) Deep Thoughts: Any idea what this consensus sequence controls? Appears that conserved domains have been shuffled during evolution to create new proteins Proteins: Conserved Domains Many proteins have multiple conserved domains 2

3 Clustal Omega: creating a multiple sequence alignment You select sequences to align from NCBI Clustal Omega: creating a multiple sequence alignment Google Clustal Omega Get FASTA sequences and copy and paste into Clustal Omega window Or put all sequences in one document (example: copy and paste into one Word document) and then copy and paste into Clustal Omega window CAN BE BUGGY L Recommend SAFARI Clustal Omega: Creating the initial alignment Generating the Sequence Files Get FASTA file for sequence 1 Copy and paste into Clustal Omega input window Hit return Get FASTA file for next sequence Copy and paste it below first sequence in ClustalW2 input window Hit return Keep repeating until get all files in window Generating the Sequence Files As you do this, prudent to record accession numbers in case of malfunction (can also keep each sequence open in separate tab) Generating the Sequence Files Can also generate word file (.doc) with all FASTA sequences copied and then copy and paste the sequences into Clustal Omega input sequence window USE SAFARI to get FASTA (less buggy) Hit return after each entry in Word; save as.doc Can be BUGGY because word programs can insert hidden characters which may cause Clustal Omega to not work L 3

4 Simple Phylogeny: creating a phylogenetic tree Simple Phylogeny can only assemble a phylogenetic tree from multiple sequence alignments generated by Clustal Omega 4

5 CHANGE! PHYLIP: Phylogeny Inference Package 5

6 Neighbor Joining Neighbor Joining Simple Phylogeny: The Cladogram A Cladogram is a branching diagram (tree) assumed to be an estimate of a phylogeny where the branches are of equal length, thus cladograms show common ancestry, but do not indicate the amount of evolutionary "time" separating taxa. Distance Value= # of substitutions as a proportion of the alignment, excluding gaps 6

THEORY. Based on sequence Length According to the length of sequence being compared it is of following two types

THEORY. Based on sequence Length According to the length of sequence being compared it is of following two types Exp 11- THEORY Sequence Alignment is a process of aligning two sequences to achieve maximum levels of identity between them. This help to derive functional, structural and evolutionary relationships between

More information

Phylogenetic analyses. Kirsi Kostamo

Phylogenetic analyses. Kirsi Kostamo Phylogenetic analyses Kirsi Kostamo The aim: To construct a visual representation (a tree) to describe the assumed evolution occurring between and among different groups (individuals, populations, species,

More information

Introduction to Bioinformatics Online Course: IBT

Introduction to Bioinformatics Online Course: IBT Introduction to Bioinformatics Online Course: IBT Multiple Sequence Alignment Building Multiple Sequence Alignment Lec1 Building a Multiple Sequence Alignment Learning Outcomes 1- Understanding Why multiple

More information

Bioinformatics tools for phylogeny and visualization. Yanbin Yin

Bioinformatics tools for phylogeny and visualization. Yanbin Yin Bioinformatics tools for phylogeny and visualization Yanbin Yin 1 Homework assignment 5 1. Take the MAFFT alignment http://cys.bios.niu.edu/yyin/teach/pbb/purdue.cellwall.list.lignin.f a.aln as input and

More information

Using Bioinformatics to Study Evolutionary Relationships Instructions

Using Bioinformatics to Study Evolutionary Relationships Instructions 3 Using Bioinformatics to Study Evolutionary Relationships Instructions Student Researcher Background: Making and Using Multiple Sequence Alignments One of the primary tasks of genetic researchers is comparing

More information

Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST

Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST Introduction Bioinformatics is a powerful tool which can be used to determine evolutionary relationships and

More information

Comparative Bioinformatics Midterm II Fall 2004

Comparative Bioinformatics Midterm II Fall 2004 Comparative Bioinformatics Midterm II Fall 2004 Objective Answer, part I: For each of the following, select the single best answer or completion of the phrase. (3 points each) 1. Deinococcus radiodurans

More information

RELATIONSHIPS BETWEEN GENES/PROTEINS HOMOLOGUES

RELATIONSHIPS BETWEEN GENES/PROTEINS HOMOLOGUES Molecular Biology-2018 1 Definitions: RELATIONSHIPS BETWEEN GENES/PROTEINS HOMOLOGUES Heterologues: Genes or proteins that possess different sequences and activities. Homologues: Genes or proteins that

More information

Journal of Proteomics & Bioinformatics - Open Access

Journal of Proteomics & Bioinformatics - Open Access Abstract Methodology for Phylogenetic Tree Construction Kudipudi Srinivas 2, Allam Appa Rao 1, GR Sridhar 3, Srinubabu Gedela 1* 1 International Center for Bioinformatics & Center for Biotechnology, Andhra

More information

Phylogenetics - Orthology, phylogenetic experimental design and phylogeny reconstruction. Lesser Tenrec (Echinops telfairi)

Phylogenetics - Orthology, phylogenetic experimental design and phylogeny reconstruction. Lesser Tenrec (Echinops telfairi) Phylogenetics - Orthology, phylogenetic experimental design and phylogeny reconstruction Lesser Tenrec (Echinops telfairi) Goals: 1. Use phylogenetic experimental design theory to select optimal taxa to

More information

Supplemental Materials

Supplemental Materials JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION, May 2013, p. 107-109 DOI: http://dx.doi.org/10.1128/jmbe.v14i1.496 Supplemental Materials for Engaging Students in a Bioinformatics Activity to Introduce Gene

More information

"Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky

Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky MOLECULAR PHYLOGENY "Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky EVOLUTION - theory that groups of organisms change over time so that descendeants differ structurally

More information

Algorithms in Bioinformatics FOUR Pairwise Sequence Alignment. Pairwise Sequence Alignment. Convention: DNA Sequences 5. Sequence Alignment

Algorithms in Bioinformatics FOUR Pairwise Sequence Alignment. Pairwise Sequence Alignment. Convention: DNA Sequences 5. Sequence Alignment Algorithms in Bioinformatics FOUR Sami Khuri Department of Computer Science San José State University Pairwise Sequence Alignment Homology Similarity Global string alignment Local string alignment Dot

More information

Bioinformatics Exercises

Bioinformatics Exercises Bioinformatics Exercises AP Biology Teachers Workshop Susan Cates, Ph.D. Evolution of Species Phylogenetic Trees show the relatedness of organisms Common Ancestor (Root of the tree) 1 Rooted vs. Unrooted

More information

MULTIPLE SEQUENCE ALIGNMENT FOR CONSTRUCTION OF PHYLOGENETIC TREE

MULTIPLE SEQUENCE ALIGNMENT FOR CONSTRUCTION OF PHYLOGENETIC TREE MULTIPLE SEQUENCE ALIGNMENT FOR CONSTRUCTION OF PHYLOGENETIC TREE Manmeet Kaur 1, Navneet Kaur Bawa 2 1 M-tech research scholar (CSE Dept) ACET, Manawala,Asr 2 Associate Professor (CSE Dept) ACET, Manawala,Asr

More information

Tree Building Activity

Tree Building Activity Tree Building Activity Introduction In this activity, you will construct phylogenetic trees using a phenotypic similarity (cartoon microbe pictures) and genotypic similarity (real microbe sequences). For

More information

Homology and Information Gathering and Domain Annotation for Proteins

Homology and Information Gathering and Domain Annotation for Proteins Homology and Information Gathering and Domain Annotation for Proteins Outline Homology Information Gathering for Proteins Domain Annotation for Proteins Examples and exercises The concept of homology The

More information

Week 10: Homology Modelling (II) - HHpred

Week 10: Homology Modelling (II) - HHpred Week 10: Homology Modelling (II) - HHpred Course: Tools for Structural Biology Fabian Glaser BKU - Technion 1 2 Identify and align related structures by sequence methods is not an easy task All comparative

More information

Introduction to Bioinformatics Introduction to Bioinformatics

Introduction to Bioinformatics Introduction to Bioinformatics Dr. rer. nat. Gong Jing Cancer Research Center Medicine School of Shandong University 2012.11.09 1 Chapter 4 Phylogenetic Tree 2 Phylogeny Evidence from morphological ( 形态学的 ), biochemical, and gene sequence

More information

Emily Blanton Phylogeny Lab Report May 2009

Emily Blanton Phylogeny Lab Report May 2009 Introduction It is suggested through scientific research that all living organisms are connected- that we all share a common ancestor and that, through time, we have all evolved from the same starting

More information

1 Abstract. 2 Introduction. 3 Requirements. 4 Procedure

1 Abstract. 2 Introduction. 3 Requirements. 4 Procedure 1 Abstract None 2 Introduction The archaeal core set is used in testing the completeness of the archaeal draft genomes. The core set comprises of conserved single copy genes from 25 genomes. Coverage statistic

More information

Comparing whole genomes

Comparing whole genomes BioNumerics Tutorial: Comparing whole genomes 1 Aim The Chromosome Comparison window in BioNumerics has been designed for large-scale comparison of sequences of unlimited length. In this tutorial you will

More information

Heuristic Alignment and Searching

Heuristic Alignment and Searching 3/28/2012 Types of alignments Global Alignment Each letter of each sequence is aligned to a letter or a gap (e.g., Needleman-Wunsch). Local Alignment An optimal pair of subsequences is taken from the two

More information

Module: Sequence Alignment Theory and Applications Session: Introduction to Searching and Sequence Alignment

Module: Sequence Alignment Theory and Applications Session: Introduction to Searching and Sequence Alignment Module: Sequence Alignment Theory and Applications Session: Introduction to Searching and Sequence Alignment Introduction to Bioinformatics online course : IBT Jonathan Kayondo Learning Objectives Understand

More information

Dr. Amira A. AL-Hosary

Dr. Amira A. AL-Hosary Phylogenetic analysis Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic Basics: Biological

More information

5. MULTIPLE SEQUENCE ALIGNMENT BIOINFORMATICS COURSE MTAT

5. MULTIPLE SEQUENCE ALIGNMENT BIOINFORMATICS COURSE MTAT 5. MULTIPLE SEQUENCE ALIGNMENT BIOINFORMATICS COURSE MTAT.03.239 03.10.2012 ALIGNMENT Alignment is the task of locating equivalent regions of two or more sequences to maximize their similarity. Homology:

More information

Sara C. Madeira. Universidade da Beira Interior. (Thanks to Ana Teresa Freitas, IST for useful resources on this subject)

Sara C. Madeira. Universidade da Beira Interior. (Thanks to Ana Teresa Freitas, IST for useful resources on this subject) Bioinformática Sequence Alignment Pairwise Sequence Alignment Universidade da Beira Interior (Thanks to Ana Teresa Freitas, IST for useful resources on this subject) 1 16/3/29 & 23/3/29 27/4/29 Outline

More information

METHODS FOR DETERMINING PHYLOGENY. In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task.

METHODS FOR DETERMINING PHYLOGENY. In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task. Chapter 12 (Strikberger) Molecular Phylogenies and Evolution METHODS FOR DETERMINING PHYLOGENY In Chapter 11, we discovered that classifying organisms into groups was, and still is, a difficult task. Modern

More information

BME 5742 Biosystems Modeling and Control

BME 5742 Biosystems Modeling and Control BME 5742 Biosystems Modeling and Control Lecture 24 Unregulated Gene Expression Model Dr. Zvi Roth (FAU) 1 The genetic material inside a cell, encoded in its DNA, governs the response of a cell to various

More information

Hands-On Nine The PAX6 Gene and Protein

Hands-On Nine The PAX6 Gene and Protein Hands-On Nine The PAX6 Gene and Protein Main Purpose of Hands-On Activity: Using bioinformatics tools to examine the sequences, homology, and disease relevance of the Pax6: a master gene of eye formation.

More information

Constructing Evolutionary/Phylogenetic Trees

Constructing Evolutionary/Phylogenetic Trees Constructing Evolutionary/Phylogenetic Trees 2 broad categories: Distance-based methods Ultrametric Additive: UPGMA Transformed Distance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood

More information

8/23/2014. Phylogeny and the Tree of Life

8/23/2014. Phylogeny and the Tree of Life Phylogeny and the Tree of Life Chapter 26 Objectives Explain the following characteristics of the Linnaean system of classification: a. binomial nomenclature b. hierarchical classification List the major

More information

Session 5: Phylogenomics

Session 5: Phylogenomics Session 5: Phylogenomics B.- Phylogeny based orthology assignment REMINDER: Gene tree reconstruction is divided in three steps: homology search, multiple sequence alignment and model selection plus tree

More information

Phylogenies Scores for Exhaustive Maximum Likelihood and Parsimony Scores Searches

Phylogenies Scores for Exhaustive Maximum Likelihood and Parsimony Scores Searches Int. J. Bioinformatics Research and Applications, Vol. x, No. x, xxxx Phylogenies Scores for Exhaustive Maximum Likelihood and s Searches Hyrum D. Carroll, Perry G. Ridge, Mark J. Clement, Quinn O. Snell

More information

Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut

Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic analysis Phylogenetic Basics: Biological

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION Supplementary information S3 (box) Methods Methods Genome weighting The currently available collection of archaeal and bacterial genomes has a highly biased distribution of isolates across taxa. For example,

More information

POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics

POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics - in deriving a phylogeny our goal is simply to reconstruct the historical relationships between a group of taxa. - before we review the

More information

BLAST. Varieties of BLAST

BLAST. Varieties of BLAST BLAST Basic Local Alignment Search Tool (1990) Altschul, Gish, Miller, Myers, & Lipman Uses short-cuts or heuristics to improve search speed Like speed-reading, does not examine every nucleotide of database

More information

Comparative genomics: Overview & Tools + MUMmer algorithm

Comparative genomics: Overview & Tools + MUMmer algorithm Comparative genomics: Overview & Tools + MUMmer algorithm Urmila Kulkarni-Kale Bioinformatics Centre University of Pune, Pune 411 007. urmila@bioinfo.ernet.in Genome sequence: Fact file 1995: The first

More information

Chapter 17. Table of Contents. Objectives. Taxonomy. Classifying Organisms. Section 1 Biodiversity. Section 2 Systematics

Chapter 17. Table of Contents. Objectives. Taxonomy. Classifying Organisms. Section 1 Biodiversity. Section 2 Systematics Classification Table of Contents Objectives Relatebiodiversity to biological classification. Explainwhy naturalists replaced Aristotle s classification system. Identifythe main criterion that Linnaeus

More information

Chapter 19 Organizing Information About Species: Taxonomy and Cladistics

Chapter 19 Organizing Information About Species: Taxonomy and Cladistics Chapter 19 Organizing Information About Species: Taxonomy and Cladistics An unexpected family tree. What are the evolutionary relationships among a human, a mushroom, and a tulip? Molecular systematics

More information

SCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION. Using Anatomy, Embryology, Biochemistry, and Paleontology

SCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION. Using Anatomy, Embryology, Biochemistry, and Paleontology SCIENTIFIC EVIDENCE TO SUPPORT THE THEORY OF EVOLUTION Using Anatomy, Embryology, Biochemistry, and Paleontology Scientific Fields Different fields of science have contributed evidence for the theory of

More information

Homology. and. Information Gathering and Domain Annotation for Proteins

Homology. and. Information Gathering and Domain Annotation for Proteins Homology and Information Gathering and Domain Annotation for Proteins Outline WHAT IS HOMOLOGY? HOW TO GATHER KNOWN PROTEIN INFORMATION? HOW TO ANNOTATE PROTEIN DOMAINS? EXAMPLES AND EXERCISES Homology

More information

Multiple sequence alignment

Multiple sequence alignment Multiple sequence alignment Multiple sequence alignment: today s goals to define what a multiple sequence alignment is and how it is generated; to describe profile HMMs to introduce databases of multiple

More information

Constructing Evolutionary/Phylogenetic Trees

Constructing Evolutionary/Phylogenetic Trees Constructing Evolutionary/Phylogenetic Trees 2 broad categories: istance-based methods Ultrametric Additive: UPGMA Transformed istance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood

More information

Phylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other?

Phylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Phylogeny: the evolutionary history of a species

More information

C3020 Molecular Evolution. Exercises #3: Phylogenetics

C3020 Molecular Evolution. Exercises #3: Phylogenetics C3020 Molecular Evolution Exercises #3: Phylogenetics Consider the following sequences for five taxa 1-5 and the known outgroup O, which has the ancestral states (note that sequence 3 has changed from

More information

Genomics and bioinformatics summary. Finding genes -- computer searches

Genomics and bioinformatics summary. Finding genes -- computer searches Genomics and bioinformatics summary 1. Gene finding: computer searches, cdnas, ESTs, 2. Microarrays 3. Use BLAST to find homologous sequences 4. Multiple sequence alignments (MSAs) 5. Trees quantify sequence

More information

Homology Modeling. Roberto Lins EPFL - summer semester 2005

Homology Modeling. Roberto Lins EPFL - summer semester 2005 Homology Modeling Roberto Lins EPFL - summer semester 2005 Disclaimer: course material is mainly taken from: P.E. Bourne & H Weissig, Structural Bioinformatics; C.A. Orengo, D.T. Jones & J.M. Thornton,

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION Supplementary information S1 (box). Supplementary Methods description. Prokaryotic Genome Database Archaeal and bacterial genome sequences were downloaded from the NCBI FTP site (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)

More information

Bioinformatics. Dept. of Computational Biology & Bioinformatics

Bioinformatics. Dept. of Computational Biology & Bioinformatics Bioinformatics Dept. of Computational Biology & Bioinformatics 3 Bioinformatics - play with sequences & structures Dept. of Computational Biology & Bioinformatics 4 ORGANIZATION OF LIFE ROLE OF BIOINFORMATICS

More information

CHAPTERS 24-25: Evidence for Evolution and Phylogeny

CHAPTERS 24-25: Evidence for Evolution and Phylogeny CHAPTERS 24-25: Evidence for Evolution and Phylogeny 1. For each of the following, indicate how it is used as evidence of evolution by natural selection or shown as an evolutionary trend: a. Paleontology

More information

Grundlagen der Bioinformatik Summer semester Lecturer: Prof. Daniel Huson

Grundlagen der Bioinformatik Summer semester Lecturer: Prof. Daniel Huson Grundlagen der Bioinformatik, SS 10, D. Huson, April 12, 2010 1 1 Introduction Grundlagen der Bioinformatik Summer semester 2010 Lecturer: Prof. Daniel Huson Office hours: Thursdays 17-18h (Sand 14, C310a)

More information

GCD3033:Cell Biology. Transcription

GCD3033:Cell Biology. Transcription Transcription Transcription: DNA to RNA A) production of complementary strand of DNA B) RNA types C) transcription start/stop signals D) Initiation of eukaryotic gene expression E) transcription factors

More information

Sequencing alignment Ameer Effat M. Elfarash

Sequencing alignment Ameer Effat M. Elfarash Sequencing alignment Ameer Effat M. Elfarash Dept. of Genetics Fac. of Agriculture, Assiut Univ. aelfarash@aun.edu.eg Why perform a multiple sequence alignment? MSAs are at the heart of comparative genomics

More information

Motifs, Profiles and Domains. Michael Tress Protein Design Group Centro Nacional de Biotecnología, CSIC

Motifs, Profiles and Domains. Michael Tress Protein Design Group Centro Nacional de Biotecnología, CSIC Motifs, Profiles and Domains Michael Tress Protein Design Group Centro Nacional de Biotecnología, CSIC Comparing Two Proteins Sequence Alignment Determining the pattern of evolution and identifying conserved

More information

(Lys), resulting in translation of a polypeptide without the Lys amino acid. resulting in translation of a polypeptide without the Lys amino acid.

(Lys), resulting in translation of a polypeptide without the Lys amino acid. resulting in translation of a polypeptide without the Lys amino acid. 1. A change that makes a polypeptide defective has been discovered in its amino acid sequence. The normal and defective amino acid sequences are shown below. Researchers are attempting to reproduce the

More information

3.B.1 Gene Regulation. Gene regulation results in differential gene expression, leading to cell specialization.

3.B.1 Gene Regulation. Gene regulation results in differential gene expression, leading to cell specialization. 3.B.1 Gene Regulation Gene regulation results in differential gene expression, leading to cell specialization. We will focus on gene regulation in prokaryotes first. Gene regulation accounts for some of

More information

Chapter 17. From Gene to Protein. Biology Kevin Dees

Chapter 17. From Gene to Protein. Biology Kevin Dees Chapter 17 From Gene to Protein DNA The information molecule Sequences of bases is a code DNA organized in to chromosomes Chromosomes are organized into genes What do the genes actually say??? Reflecting

More information

PHYLOGENY AND SYSTEMATICS

PHYLOGENY AND SYSTEMATICS AP BIOLOGY EVOLUTION/HEREDITY UNIT Unit 1 Part 11 Chapter 26 Activity #15 NAME DATE PERIOD PHYLOGENY AND SYSTEMATICS PHYLOGENY Evolutionary history of species or group of related species SYSTEMATICS Study

More information

COMPARING DNA SEQUENCES TO UNDERSTAND EVOLUTIONARY RELATIONSHIPS WITH BLAST

COMPARING DNA SEQUENCES TO UNDERSTAND EVOLUTIONARY RELATIONSHIPS WITH BLAST Big Idea 1 Evolution INVESTIGATION 3 COMPARING DNA SEQUENCES TO UNDERSTAND EVOLUTIONARY RELATIONSHIPS WITH BLAST How can bioinformatics be used as a tool to determine evolutionary relationships and to

More information

Chapter 19: Taxonomy, Systematics, and Phylogeny

Chapter 19: Taxonomy, Systematics, and Phylogeny Chapter 19: Taxonomy, Systematics, and Phylogeny AP Curriculum Alignment Chapter 19 expands on the topics of phylogenies and cladograms, which are important to Big Idea 1. In order for students to understand

More information

Effects of Gap Open and Gap Extension Penalties

Effects of Gap Open and Gap Extension Penalties Brigham Young University BYU ScholarsArchive All Faculty Publications 200-10-01 Effects of Gap Open and Gap Extension Penalties Hyrum Carroll hyrumcarroll@gmail.com Mark J. Clement clement@cs.byu.edu See

More information

The Phylogenetic Handbook

The Phylogenetic Handbook The Phylogenetic Handbook A Practical Approach to DNA and Protein Phylogeny Edited by Marco Salemi University of California, Irvine and Katholieke Universiteit Leuven, Belgium and Anne-Mieke Vandamme Rega

More information

MiGA: The Microbial Genome Atlas

MiGA: The Microbial Genome Atlas December 12 th 2017 MiGA: The Microbial Genome Atlas Jim Cole Center for Microbial Ecology Dept. of Plant, Soil & Microbial Sciences Michigan State University East Lansing, Michigan U.S.A. Where I m From

More information

BIOINFORMATICS LAB AP BIOLOGY

BIOINFORMATICS LAB AP BIOLOGY BIOINFORMATICS LAB AP BIOLOGY Bioinformatics is the science of collecting and analyzing complex biological data. Bioinformatics combines computer science, statistics and biology to allow scientists to

More information

InDel 3-5. InDel 8-9. InDel 3-5. InDel 8-9. InDel InDel 8-9

InDel 3-5. InDel 8-9. InDel 3-5. InDel 8-9. InDel InDel 8-9 Lecture 5 Alignment I. Introduction. For sequence data, the process of generating an alignment establishes positional homologies; that is, alignment provides the identification of homologous phylogenetic

More information

Protein Bioinformatics. Rickard Sandberg Dept. of Cell and Molecular Biology Karolinska Institutet sandberg.cmb.ki.

Protein Bioinformatics. Rickard Sandberg Dept. of Cell and Molecular Biology Karolinska Institutet sandberg.cmb.ki. Protein Bioinformatics Rickard Sandberg Dept. of Cell and Molecular Biology Karolinska Institutet rickard.sandberg@ki.se sandberg.cmb.ki.se Outline Protein features motifs patterns profiles signals 2 Protein

More information

Processes of Evolution

Processes of Evolution 15 Processes of Evolution Forces of Evolution Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive Natural selection can act on quantitative traits in three ways: Stabilizing selection

More information

Large-Scale Genomic Surveys

Large-Scale Genomic Surveys Bioinformatics Subtopics Fold Recognition Secondary Structure Prediction Docking & Drug Design Protein Geometry Protein Flexibility Homology Modeling Sequence Alignment Structure Classification Gene Prediction

More information

Statistical Machine Learning Methods for Biomedical Informatics II. Hidden Markov Model for Biological Sequences

Statistical Machine Learning Methods for Biomedical Informatics II. Hidden Markov Model for Biological Sequences Statistical Machine Learning Methods for Biomedical Informatics II. Hidden Markov Model for Biological Sequences Jianlin Cheng, PhD William and Nancy Thompson Missouri Distinguished Professor Department

More information

Molecular phylogeny - Using molecular sequences to infer evolutionary relationships. Tore Samuelsson Feb 2016

Molecular phylogeny - Using molecular sequences to infer evolutionary relationships. Tore Samuelsson Feb 2016 Molecular phylogeny - Using molecular sequences to infer evolutionary relationships Tore Samuelsson Feb 2016 Molecular phylogeny is being used in the identification and characterization of new pathogens,

More information

Statistical Machine Learning Methods for Bioinformatics II. Hidden Markov Model for Biological Sequences

Statistical Machine Learning Methods for Bioinformatics II. Hidden Markov Model for Biological Sequences Statistical Machine Learning Methods for Bioinformatics II. Hidden Markov Model for Biological Sequences Jianlin Cheng, PhD Department of Computer Science University of Missouri 2008 Free for Academic

More information

Basic Local Alignment Search Tool

Basic Local Alignment Search Tool Basic Local Alignment Search Tool Alignments used to uncover homologies between sequences combined with phylogenetic studies o can determine orthologous and paralogous relationships Local Alignment uses

More information

Chapter 26: Phylogeny and the Tree of Life Phylogenies Show Evolutionary Relationships

Chapter 26: Phylogeny and the Tree of Life Phylogenies Show Evolutionary Relationships Chapter 26: Phylogeny and the Tree of Life You Must Know The taxonomic categories and how they indicate relatedness. How systematics is used to develop phylogenetic trees. How to construct a phylogenetic

More information

CONCEPT OF SEQUENCE COMPARISON. Natapol Pornputtapong 18 January 2018

CONCEPT OF SEQUENCE COMPARISON. Natapol Pornputtapong 18 January 2018 CONCEPT OF SEQUENCE COMPARISON Natapol Pornputtapong 18 January 2018 SEQUENCE ANALYSIS - A ROSETTA STONE OF LIFE Sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of

More information

3. SEQUENCE ANALYSIS BIOINFORMATICS COURSE MTAT

3. SEQUENCE ANALYSIS BIOINFORMATICS COURSE MTAT 3. SEQUENCE ANALYSIS BIOINFORMATICS COURSE MTAT.03.239 25.09.2012 SEQUENCE ANALYSIS IS IMPORTANT FOR... Prediction of function Gene finding the process of identifying the regions of genomic DNA that encode

More information

Cladistics and Bioinformatics Questions 2013

Cladistics and Bioinformatics Questions 2013 AP Biology Name Cladistics and Bioinformatics Questions 2013 1. The following table shows the percentage similarity in sequences of nucleotides from a homologous gene derived from five different species

More information

BLAST Database Searching. BME 110: CompBio Tools Todd Lowe April 8, 2010

BLAST Database Searching. BME 110: CompBio Tools Todd Lowe April 8, 2010 BLAST Database Searching BME 110: CompBio Tools Todd Lowe April 8, 2010 Admin Reading: Read chapter 7, and the NCBI Blast Guide and tutorial http://www.ncbi.nlm.nih.gov/blast/why.shtml Read Chapter 8 for

More information

In-Depth Assessment of Local Sequence Alignment

In-Depth Assessment of Local Sequence Alignment 2012 International Conference on Environment Science and Engieering IPCBEE vol.3 2(2012) (2012)IACSIT Press, Singapoore In-Depth Assessment of Local Sequence Alignment Atoosa Ghahremani and Mahmood A.

More information

Inferring phylogeny. Constructing phylogenetic trees. Tõnu Margus. Bioinformatics MTAT

Inferring phylogeny. Constructing phylogenetic trees. Tõnu Margus. Bioinformatics MTAT Inferring phylogeny Constructing phylogenetic trees Tõnu Margus Contents What is phylogeny? How/why it is possible to infer it? Representing evolutionary relationships on trees What type questions questions

More information

Biodiversity. The Road to the Six Kingdoms of Life

Biodiversity. The Road to the Six Kingdoms of Life Biodiversity The Road to the Six Kingdoms of Life How the 6 kingdoms came about At first, only two kingdoms were recognized Then Haeckel proposed a third kingdom Protista (where protists had both plant

More information

GEP Annotation Report

GEP Annotation Report GEP Annotation Report Note: For each gene described in this annotation report, you should also prepare the corresponding GFF, transcript and peptide sequence files as part of your submission. Student name:

More information

Quantifying sequence similarity

Quantifying sequence similarity Quantifying sequence similarity Bas E. Dutilh Systems Biology: Bioinformatic Data Analysis Utrecht University, February 16 th 2016 After this lecture, you can define homology, similarity, and identity

More information

Molecular phylogeny How to infer phylogenetic trees using molecular sequences

Molecular phylogeny How to infer phylogenetic trees using molecular sequences Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 2009 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues

More information

- conserved in Eukaryotes. - proteins in the cluster have identifiable conserved domains. - human gene should be included in the cluster.

- conserved in Eukaryotes. - proteins in the cluster have identifiable conserved domains. - human gene should be included in the cluster. NCBI BLAST Services DELTA-BLAST BLAST (http://blast.ncbi.nlm.nih.gov/), Basic Local Alignment Search tool, is a suite of programs for finding similarities between biological sequences. DELTA-BLAST is a

More information

Some of these slides have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks!

Some of these slides have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks! Some of these slides have been borrowed from Dr. Paul Lewis, Dr. Joe Felsenstein. Thanks! Paul has many great tools for teaching phylogenetics at his web site: http://hydrodictyon.eeb.uconn.edu/people/plewis

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION doi:10.1038/nature11510 Supplementary Table 1. Indel Index Removal Gene Number of Starting Sequences Number of Final Sequences Percentage of Sequences Removed based on the Indel

More information

Basics on bioinforma-cs Lecture 7. Nunzio D Agostino

Basics on bioinforma-cs Lecture 7. Nunzio D Agostino Basics on bioinforma-cs Lecture 7 Nunzio D Agostino nunzio.dagostino@entecra.it; nunzio.dagostino@gmail.com Multiple alignments One sequence plays coy a pair of homologous sequence whisper many aligned

More information

Orthology Part I concepts and implications Toni Gabaldón Centre for Genomic Regulation (CRG), Barcelona

Orthology Part I concepts and implications Toni Gabaldón Centre for Genomic Regulation (CRG), Barcelona Orthology Part I concepts and implications Toni Gabaldón Centre for Genomic Regulation (CRG), Barcelona Toni Gabaldón Contact: tgabaldon@crg.es Group website: http://gabaldonlab.crg.es Science blog: http://treevolution.blogspot.com

More information

Phylogeny: building the tree of life

Phylogeny: building the tree of life Phylogeny: building the tree of life Dr. Fayyaz ul Amir Afsar Minhas Department of Computer and Information Sciences Pakistan Institute of Engineering & Applied Sciences PO Nilore, Islamabad, Pakistan

More information

UNIT 5. Protein Synthesis 11/22/16

UNIT 5. Protein Synthesis 11/22/16 UNIT 5 Protein Synthesis IV. Transcription (8.4) A. RNA carries DNA s instruction 1. Francis Crick defined the central dogma of molecular biology a. Replication copies DNA b. Transcription converts DNA

More information

Phylogenetics: Building Phylogenetic Trees

Phylogenetics: Building Phylogenetic Trees 1 Phylogenetics: Building Phylogenetic Trees COMP 571 Luay Nakhleh, Rice University 2 Four Questions Need to be Answered What data should we use? Which method should we use? Which evolutionary model should

More information

Chapter 20. Initiation of transcription. Eukaryotic transcription initiation

Chapter 20. Initiation of transcription. Eukaryotic transcription initiation Chapter 20. Initiation of transcription Eukaryotic transcription initiation 2003. 5.22 Prokaryotic vs eukaryotic Bacteria = one RNA polymerase Eukaryotes have three RNA polymerases (I, II, and III) in

More information

Phylogenetic Tree Generation using Different Scoring Methods

Phylogenetic Tree Generation using Different Scoring Methods International Journal of Computer Applications (975 8887) Phylogenetic Tree Generation using Different Scoring Methods Rajbir Singh Associate Prof. & Head Department of IT LLRIET, Moga Sinapreet Kaur Student

More information

Name: Class: Date: ID: A

Name: Class: Date: ID: A Class: _ Date: _ Ch 17 Practice test 1. A segment of DNA that stores genetic information is called a(n) a. amino acid. b. gene. c. protein. d. intron. 2. In which of the following processes does change

More information

Molecular phylogeny How to infer phylogenetic trees using molecular sequences

Molecular phylogeny How to infer phylogenetic trees using molecular sequences Molecular phylogeny How to infer phylogenetic trees using molecular sequences ore Samuelsson Nov 200 Applications of phylogenetic methods Reconstruction of evolutionary history / Resolving taxonomy issues

More information

Single alignment: Substitution Matrix. 16 march 2017

Single alignment: Substitution Matrix. 16 march 2017 Single alignment: Substitution Matrix 16 march 2017 BLOSUM Matrix BLOSUM Matrix [2] (Blocks Amino Acid Substitution Matrices ) It is based on the amino acids substitutions observed in ~2000 conserved block

More information

Building 3D models of proteins

Building 3D models of proteins Building 3D models of proteins Why make a structural model for your protein? The structure can provide clues to the function through structural similarity with other proteins With a structure it is easier

More information