DATA ACQUISITION FROM BIO-DATABASES AND BLAST. Natapol Pornputtapong 18 January 2018
|
|
- Brent Lynch
- 5 years ago
- Views:
Transcription
1 DATA ACQUISITION FROM BIO-DATABASES AND BLAST Natapol Pornputtapong 18 January 2018
2 DATABASE Collections of data To share multi-user interface To prevent data loss To make sure to get the right things Bioinformatics for Phylogenetic Analysis Workshop 2
3 LIBRARY -> DIGITAL LIBRARY Bioinformatics for Phylogenetic Analysis Workshop 3
4 DATABASE: A LIBRARY OF DATA Database Files, Tables, Records Data structure Database management system Programming interface User interface Library Books building, shelves Librarian Protocols, SOPs Services Bioinformatics for Phylogenetic Analysis Workshop 4
5 ADVANTAGE OF DATABASE Data integrity Smaller space Data availability Speed Bioinformatics for Phylogenetic Analysis Workshop 5
6 DATABASE FOR USERS Search Database Download Users Submission Bioinformatics for Phylogenetic Analysis Workshop 6
7 HOW TO CHOOSE DATABASE? 1695 bio-databases in NAR online Molecular Biology Database Collection in 15 categories Bioinformatics for Phylogenetic Analysis Workshop 7
8 DATA CONTENT Literature DNA sequence GenBank Protein sequence RefSeq TrEMBL Bioinformatics for Phylogenetic Analysis Workshop 8
9 CONCEPTS OF DATABASE Primary database Secondary database interface interface Database Database Database Database Database Source Source Source Bioinformatics for Phylogenetic Analysis Workshop 9
10 PRIMARY & SECONDARY DB Primary database Secondary database Synonyms Archival database Curated database; knowledgebase Source of data Examples Direct submission of experimentally-derived data from researchers ENA, GenBank and DDBJ (nucleoti de sequence) ArrayExpress Archive and GEO (functional genomics data) Protein Data Bank (PDB; coordinates of three-dimensional macromolecular structures) Results of analysis, literature research and interpretation, often of data in primary databases InterPro (protein families, motifs and domains) UniProt Knowledgebase (sequence and functional information on proteins) Ensembl (variation, function, regulation and more layered onto whole genome sequences) Bioinformatics for Phylogenetic Analysis Workshop 10
11 DATA COLLECTION CRITERIA GenBank RefSeq GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences Bioinformatics for Phylogenetic Analysis Workshop 11
12 Bioinformatics for Phylogenetic Analysis Workshop 12
13 ACCESSIBILITY: TOOLS & INTERFACES NCBI Entrez RESTful interface to the ENA Bioinformatics for Phylogenetic Analysis Workshop 13
14 NCBI SEARCH TOOL Bioinformatics for Phylogenetic Analysis Workshop 14
15 SIMPLE SEARCH Bioinformatics for Phylogenetic Analysis Workshop 15
16 BOOLEAN OPERATOR Bioinformatics for Phylogenetic Analysis Workshop 16
17 FILTER Limit with filter Advanced search builder Bioinformatics for Phylogenetic Analysis Workshop 17
18 RESULTS Bioinformatics for Phylogenetic Analysis Workshop 18
19 BLAST: BASIC LOCAL ALIGNMENT SEARCH TOOL Bioinformatics for Phylogenetic Analysis Workshop 19
20 MAJOR BLAST PROGRAMS Bioinformatics for Phylogenetic Analysis Workshop 20
21 BLAST SEARCH Bioinformatics for Phylogenetic Analysis Workshop 21
22 Bioinformatics for Phylogenetic Analysis Workshop 22
23 OTHER BLAST PROGRAMS Bioinformatics for Phylogenetic Analysis Workshop 23
24 WORLD OF FILES Text files Binary files Bioinformatics for Phylogenetic Analysis Workshop 24
25 TEXT FILES: WORLD OF FORMATS MS Words:.doc,.docx,.rtf,.txt Sequence: FastA (.fasta), Genbank (.gbk) Protein structure: PDB (.pdb) Bioinformatics for Phylogenetic Analysis Workshop 25
26 FASTA FORMAT >P01013 GENE X PROTEIN (OVALBUMIN-RELATED) QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMP FHVTKQESKPVQMMCMNNSFNVATLPAEKMKILELPFASGDL SMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVY LPQMKIEEKYNLTSVLMALGMTDLFIPSANLTGISSAESLKI SQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP FLFLIKHNPTNTIVYFGRYWSP > Bioinformatics for Phylogenetic Analysis Workshop 26
27 GENBANK FORMAT Bioinformatics for Phylogenetic Analysis Workshop 27
28 NEXUS FORMAT #NEXUS BEGIN DATA; DIMENSIONS NTAX=8 NCHAR=1202; FORMAT MISSING=? DATATYPE=PROTEIN GAP=-; OPTIONS GAPMODE=MISSING; MATRIX [ ] [ ] Homo_sapiens_ TERLVLPPPDPLDLPLRAVEL... Pan_troglodytes_ TERLVLPPPDPLDLPLRAVEL... Ailuropoda_melanoleuca_ TERLVLPPPDPLDLPLRPVEL... Mus_musculus_ TERLVLPPLDPLNLPLRALEV... Danio_rerio_ MDKIDLPPVGPDDLPLSLLEM... Xenopus_tropicalis_ MNTLDLSNRDPLDLPLSVLEL... Monodelphis_domestica_ TERLVLPPRGPLDLPLCALEL... Canis_familiaris_ TERLALPPPDPLDLPLRPVEL...; END; Bioinformatics for Phylogenetic Analysis Workshop 28
29 NEXT Inputs Analysis Results Bioinformatics for Phylogenetic Analysis Workshop 29
30 QUESTION? Bioinformatics for Phylogenetic Analysis Workshop 30
CS612 - Algorithms in Bioinformatics
Fall 2017 Databases and Protein Structure Representation October 2, 2017 Molecular Biology as Information Science > 12, 000 genomes sequenced, mostly bacterial (2013) > 5x10 6 unique sequences available
More informationBioinformatics. 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 informationHands-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 informationEBI web resources II: Ensembl and InterPro. Yanbin Yin Spring 2013
EBI web resources II: Ensembl and InterPro Yanbin Yin Spring 2013 1 Outline Intro to genome annotation Protein family/domain databases InterPro, Pfam, Superfamily etc. Genome browser Ensembl Hands on Practice
More informationBLAST 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 informationIntroduction 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 informationGenome Annotation. Bioinformatics and Computational Biology. Genome sequencing Assembly. Gene prediction. Protein targeting.
Genome Annotation Bioinformatics and Computational Biology Genome Annotation Frank Oliver Glöckner 1 Genome Analysis Roadmap Genome sequencing Assembly Gene prediction Protein targeting trna prediction
More informationGrundlagen 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 informationMathangi Thiagarajan Rice Genome Annotation Workshop May 23rd, 2007
-2 Transcript Alignment Assembly and Automated Gene Structure Improvements Using PASA-2 Mathangi Thiagarajan mathangi@jcvi.org Rice Genome Annotation Workshop May 23rd, 2007 About PASA PASA is an open
More informationNetworks & pathways. Hedi Peterson MTAT Bioinformatics
Networks & pathways Hedi Peterson (peterson@quretec.com) MTAT.03.239 Bioinformatics 03.11.2010 Networks are graphs Nodes Edges Edges Directed, undirected, weighted Nodes Genes Proteins Metabolites Enzymes
More informationUsing 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 informationWeek 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 informationCISC 889 Bioinformatics (Spring 2004) Sequence pairwise alignment (I)
CISC 889 Bioinformatics (Spring 2004) Sequence pairwise alignment (I) Contents Alignment algorithms Needleman-Wunsch (global alignment) Smith-Waterman (local alignment) Heuristic algorithms FASTA BLAST
More informationIntroduction to Bioinformatics
CSCI8980: Applied Machine Learning in Computational Biology Introduction to Bioinformatics Rui Kuang Department of Computer Science and Engineering University of Minnesota kuang@cs.umn.edu History of Bioinformatics
More informationLarge-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 informationUNDERSTANDING BIOINFORMATICS PDF
UNDERSTANDING BIOINFORMATICS PDF ==> Download: UNDERSTANDING BIOINFORMATICS PDF UNDERSTANDING BIOINFORMATICS PDF - Are you searching for Understanding Bioinformatics Books? Now, you will be happy that
More informationMitochondrial Genome Annotation
Protein Genes 1,2 1 Institute of Bioinformatics University of Leipzig 2 Department of Bioinformatics Lebanese University TBI Bled 2015 Outline Introduction Mitochondrial DNA Problem Tools Training Annotation
More informationGEP 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 informationLecture 2. The Blast2GO annotation framework
Lecture 2 The Blast2GO annotation framework Annotation steps Modulation of annotation intensity Export/Import Functions Sequence Selection Additional Tools Functional assignment Annotation Transference
More informationGiri Narasimhan. CAP 5510: Introduction to Bioinformatics CGS 5166: Bioinformatics Tools. Evaluation. Course Homepage.
CAP 5510: Introduction to Bioinformatics CGS 5166: Bioinformatics Tools Giri Narasimhan ECS 389; Phone: x3748 giri@cis.fiu.edu www.cis.fiu.edu/~giri/teach/bioinfs06.html 1/12/06 CAP5510/CGS5166 1 Evaluation
More informationSession 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 informationJournal 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 informationChapter 5. Proteomics and the analysis of protein sequence Ⅱ
Proteomics Chapter 5. Proteomics and the analysis of protein sequence Ⅱ 1 Pairwise similarity searching (1) Figure 5.5: manual alignment One of the amino acids in the top sequence has no equivalent and
More informationHomology Modeling (Comparative Structure Modeling) GBCB 5874: Problem Solving in GBCB
Homology Modeling (Comparative Structure Modeling) Aims of Structural Genomics High-throughput 3D structure determination and analysis To determine or predict the 3D structures of all the proteins encoded
More informationGenome Annotation. Qi Sun Bioinformatics Facility Cornell University
Genome Annotation Qi Sun Bioinformatics Facility Cornell University Some basic bioinformatics tools BLAST PSI-BLAST - Position-Specific Scoring Matrix HMM - Hidden Markov Model NCBI BLAST How does BLAST
More informationDomain-based computational approaches to understand the molecular basis of diseases
Domain-based computational approaches to understand the molecular basis of diseases Dr. Maricel G. Kann Assistant Professor Dept of Biological Sciences UMBC http://bioinf.umbc.edu Research at Kann s Lab.
More informationBioinformatics 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 informationIntegration of functional genomics data
Integration of functional genomics data Laboratoire Bordelais de Recherche en Informatique (UMR) Centre de Bioinformatique de Bordeaux (Plateforme) Rennes Oct. 2006 1 Observations and motivations Genomics
More information1 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 informationHomology. 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 informationHow much non-coding DNA do eukaryotes require?
How much non-coding DNA do eukaryotes require? Andrei Zinovyev UMR U900 Computational Systems Biology of Cancer Institute Curie/INSERM/Ecole de Mine Paritech Dr. Sebastian Ahnert Dr. Thomas Fink Bioinformatics
More informationSynteny Portal Documentation
Synteny Portal Documentation Synteny Portal is a web application portal for visualizing, browsing, searching and building synteny blocks. Synteny Portal provides four main web applications: SynCircos,
More informationModule: 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 informationHomology 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 informationTree 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 informationProtein function prediction based on sequence analysis
Performing sequence searches Post-Blast analysis, Using profiles and pattern-matching Protein function prediction based on sequence analysis Slides from a lecture on MOL204 - Applied Bioinformatics 18-Oct-2005
More informationIntroduction to Bioinformatics
Introduction to Bioinformatics Jianlin Cheng, PhD Department of Computer Science Informatics Institute 2011 Topics Introduction Biological Sequence Alignment and Database Search Analysis of gene expression
More informationEBI web resources II: Ensembl and InterPro
EBI web resources II: Ensembl and InterPro Yanbin Yin http://www.ebi.ac.uk/training/online/course/ 1 Homework 3 Go to http://www.ebi.ac.uk/interpro/training.htmland finish the second online training course
More informationAnnotation Error in Public Databases ALEXANDRA SCHNOES UNIVERSITY OF CALIFORNIA, SAN FRANCISCO OCTOBER 25, 2010
Annotation Error in Public Databases ALEXANDRA SCHNOES UNIVERSITY OF CALIFORNIA, SAN FRANCISCO OCTOBER 25, 2010 1 New genomes (and metagenomes) sequenced every day... 2 3 3 3 3 3 3 3 3 3 Computational
More information08/21/2017 BLAST. Multiple Sequence Alignments: Clustal Omega
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
More informationSupplementary Materials for R3P-Loc Web-server
Supplementary Materials for R3P-Loc Web-server Shibiao Wan and Man-Wai Mak email: shibiao.wan@connect.polyu.hk, enmwmak@polyu.edu.hk June 2014 Back to R3P-Loc Server Contents 1 Introduction to R3P-Loc
More informationSequences, Structures, and Gene Regulatory Networks
Sequences, Structures, and Gene Regulatory Networks Learning Outcomes After this class, you will Understand gene expression and protein structure in more detail Appreciate why biologists like to align
More informationInvestigation 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 informationPhylogenetics - 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 informationG4120: Introduction to Computational Biology
ICB Fall 2003 G4120: Introduction to Computational Biology Oliver Jovanovic, Ph.D. Columbia University Department of Microbiology Copyright 2003 Oliver Jovanovic, All Rights Reserved. Bioinformatics and
More informationHomology 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 informationEmily 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 informationComparative 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 informationAlgorithms 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 informationVMD: Visual Molecular Dynamics. Our Microscope is Made of...
VMD: Visual Molecular Dynamics Computational Microscope / Tool to Think amino acid tyrosine enzymatic control BPTI VMD tutorial traficking Ubiquitin case study http://www.ks.uiuc.edu/training/casestudies/
More informationChemical Data Retrieval and Management
Chemical Data Retrieval and Management ChEMBL, ChEBI, and the Chemistry Development Kit Stephan A. Beisken What is EMBL-EBI? Part of the European Molecular Biology Laboratory International, non-profit
More informationBLAST. 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 informationMotifs, 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 informationHeuristic 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 informationSequencing 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 informationBiology Tutorial. Aarti Balasubramani Anusha Bharadwaj Massa Shoura Stefan Giovan
Biology Tutorial Aarti Balasubramani Anusha Bharadwaj Massa Shoura Stefan Giovan Viruses A T4 bacteriophage injecting DNA into a cell. Influenza A virus Electron micrograph of HIV. Cone-shaped cores are
More informationCOMPARING 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 informationSupplementary Materials for mplr-loc Web-server
Supplementary Materials for mplr-loc Web-server Shibiao Wan and Man-Wai Mak email: shibiao.wan@connect.polyu.hk, enmwmak@polyu.edu.hk June 2014 Back to mplr-loc Server Contents 1 Introduction to mplr-loc
More informationSequencing alignment Ameer Effat M. Elfarash
Sequencing alignment Ameer Effat M. Elfarash Dept. of Genetics Fac. of Agriculture, Assiut Univ. amir_effat@yahoo.com Why perform a multiple sequence alignment? MSAs are at the heart of comparative genomics
More informationSyllabus of BIOINF 528 (2017 Fall, Bioinformatics Program)
Syllabus of BIOINF 528 (2017 Fall, Bioinformatics Program) Course Name: Structural Bioinformatics Course Description: Instructor: This course introduces fundamental concepts and methods for structural
More information1. Protein Data Bank (PDB) 1. Protein Data Bank (PDB)
Protein structure databases; visualization; and classifications 1. Introduction to Protein Data Bank (PDB) 2. Free graphic software for 3D structure visualization 3. Hierarchical classification of protein
More informationMultiple 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 informationFrancisco M. Couto Mário J. Silva Pedro Coutinho
Francisco M. Couto Mário J. Silva Pedro Coutinho DI FCUL TR 03 29 Departamento de Informática Faculdade de Ciências da Universidade de Lisboa Campo Grande, 1749 016 Lisboa Portugal Technical reports are
More informationBioinformatics. Proteins II. - Pattern, Profile, & Structure Database Searching. Robert Latek, Ph.D. Bioinformatics, Biocomputing
Bioinformatics Proteins II. - Pattern, Profile, & Structure Database Searching Robert Latek, Ph.D. Bioinformatics, Biocomputing WIBR Bioinformatics Course, Whitehead Institute, 2002 1 Proteins I.-III.
More informationUpdate on human genome completion and annotations: Protein information resource
UPDATE ON GENOME COMPLETION AND ANNOTATIONS Update on human genome completion and annotations: Protein information resource Cathy Wu 1 and Daniel W. Nebert 2 * 1 Director of PIR, Department of Biochemistry
More informationComparing 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 informationEnsembl focuses on metazoan (animal) genomes. The genomes currently available at the Ensembl site are:
Comparative genomics and proteomics Species available Ensembl focuses on metazoan (animal) genomes. The genomes currently available at the Ensembl site are: Vertebrates: human, chimpanzee, mouse, rat,
More informationSingle 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 informationPractical search strategies
Computational and Comparative Genomics Similarity Searching II Practical search strategies Bill Pearson wrp@virginia.edu 1 Protein Evolution and Sequence Similarity Similarity Searching I What is Homology
More informationIGENETICS A MOLECULAR APPROACH PDF
IGENETICS A MOLECULAR APPROACH PDF ==> Download: IGENETICS A MOLECULAR APPROACH PDF IGENETICS A MOLECULAR APPROACH PDF - Are you searching for Igenetics A Molecular Approach Books? Now, you will be happy
More informationLEHNINGER PRINCIPLES OF BIOCHEMISTRY 6TH EDITION TEST BANK PDF
LEHNINGER PRINCIPLES OF BIOCHEMISTRY 6TH EDITION TEST BANK PDF ==> Download: LEHNINGER PRINCIPLES OF BIOCHEMISTRY 6TH EDITION TEST BANK PDF LEHNINGER PRINCIPLES OF BIOCHEMISTRY 6TH EDITION TEST BANK PDF
More informationWe have: We will: Assembled six genomes Made predictions of most likely gene locations. Add a layers of biological meaning to the sequences
Recap We have: Assembled six genomes Made predictions of most likely gene locations We will: Add a layers of biological meaning to the sequences Start with Biology This will motivate the choices we make
More informationMolecular Modeling. Prediction of Protein 3D Structure from Sequence. Vimalkumar Velayudhan. May 21, 2007
Molecular Modeling Prediction of Protein 3D Structure from Sequence Vimalkumar Velayudhan Jain Institute of Vocational and Advanced Studies May 21, 2007 Vimalkumar Velayudhan Molecular Modeling 1/23 Outline
More informationSection 14 1 Human Heredity Answer Key Pages
We have made it easy for you to find a PDF Ebooks without any digging. And by having access to our ebooks online or by storing it on your computer, you have convenient answers with section 14 1 human heredity
More informationAPPLICATION OF GRAPH BASED DATA MINING TO BIOLOGICAL NETWORKS CHANG HUN YOU. Presented to the Faculty of the Graduate School of
APPLICATION OF GRAPH BASED DATA MINING TO BIOLOGICAL NETWORKS by CHANG HUN YOU Presented to the Faculty of the Graduate School of The University of Texas at Arlington in Partial Fulfillment of the Requirements
More informationFunctional Annotation
Functional Annotation Outline Introduction Strategy Pipeline Databases Now, what s next? Functional Annotation Adding the layers of analysis and interpretation necessary to extract its biological significance
More informationUSING BLAST TO IDENTIFY PROTEINS THAT ARE EVOLUTIONARILY RELATED ACROSS SPECIES
USING BLAST TO IDENTIFY PROTEINS THAT ARE EVOLUTIONARILY RELATED ACROSS SPECIES HOW CAN BIOINFORMATICS BE USED AS A TOOL TO DETERMINE EVOLUTIONARY RELATIONSHPS AND TO BETTER UNDERSTAND PROTEIN HERITAGE?
More informationAlgorithmics and Bioinformatics
Algorithmics and Bioinformatics Gregory Kucherov and Philippe Gambette LIGM/CNRS Université Paris-Est Marne-la-Vallée, France Schedule Course webpage: https://wikimpri.dptinfo.ens-cachan.fr/doku.php?id=cours:c-1-32
More informationINTRODUCTION TO GENETIC ANALYSIS 10TH EDITION TEST BANK PDF
INTRODUCTION TO GENETIC ANALYSIS 10TH EDITION TEST BANK PDF ==> Download: INTRODUCTION TO GENETIC ANALYSIS 10TH EDITION TEST BANK PDF INTRODUCTION TO GENETIC ANALYSIS 10TH EDITION TEST BANK PDF - Are you
More informationSara 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 informationProtoNet 4.0: A hierarchical classification of one million protein sequences
ProtoNet 4.0: A hierarchical classification of one million protein sequences Noam Kaplan 1*, Ori Sasson 2, Uri Inbar 2, Moriah Friedlich 2, Menachem Fromer 2, Hillel Fleischer 2, Elon Portugaly 2, Nathan
More informationBIOINFORMATICS: METHODS AND APPLICATIONS: (Genomics, Proteomics and Drug Discovery)
BIOINFORMATICS: METHODS AND APPLICATIONS: (Genomics, Proteomics and Drug Discovery) S. C. RASTOGI, NAMITA MENDIRATTA, PARAG RASTOGI Click here if your download doesn"t start automatically BIOINFORMATICS:
More informationBioinformatics 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-max_target_seqs: maximum number of targets to report
Review of exercise 1 tblastn -num_threads 2 -db contig -query DH10B.fasta -out blastout.xls -evalue 1e-10 -outfmt "6 qseqid sseqid qstart qend sstart send length nident pident evalue" Other options: -max_target_seqs:
More informationProtein Quantitation II: Multiple Reaction Monitoring. Kelly Ruggles New York University
Protein Quantitation II: Multiple Reaction Monitoring Kelly Ruggles kelly@fenyolab.org New York University Traditional Affinity-based proteomics Use antibodies to quantify proteins Western Blot RPPA Immunohistochemistry
More informationInvestigating Evolutionary Questions Using Online Molecular Databases *
Investigating Evolutionary Questions Using Online Molecular Databases * Adapted from Puterbaugh and Burleigh, and The American Biology Teacher Lesson Background and Overview [Student Information Handout]
More informationATLAS of Biochemistry
ATLAS of Biochemistry USER GUIDE http://lcsb-databases.epfl.ch/atlas/ CONTENT 1 2 3 GET STARTED Create your user account NAVIGATE Curated KEGG reactions ATLAS reactions Pathways Maps USE IT! Fill a gap
More informationBioinformatics Chapter 1. Introduction
Bioinformatics Chapter 1. Introduction Outline! Biological Data in Digital Symbol Sequences! Genomes Diversity, Size, and Structure! Proteins and Proteomes! On the Information Content of Biological Sequences!
More informationPogil Biology Activities Evidence For Evolution
Pogil Biology Activities Free PDF ebook Download: Pogil Biology Activities Download or Read Online ebook pogil biology activities evidence for evolution in PDF Format From The Best User Guide Database
More informationPLANT BIOLOGY GRAHAM PDF
PLANT BIOLOGY GRAHAM PDF ==> Download: PLANT BIOLOGY GRAHAM PDF PLANT BIOLOGY GRAHAM PDF - Are you searching for Plant Biology Graham Books? Now, you will be happy that at this time Plant Biology Graham
More informationCONCEPT 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 informationThe Contribution of Bioinformatics to Evolutionary Thought
The Contribution of Bioinformatics to Evolutionary Thought A demonstration of the abilities of Entrez, BLAST, and UCSC s Genome Browser to provide information about common ancestry. American Scientific
More informationTRANSCRIPTION VS TRANSLATION FILE
23 April, 2018 TRANSCRIPTION VS TRANSLATION FILE Document Filetype: PDF 352.85 KB 0 TRANSCRIPTION VS TRANSLATION FILE Get an answer for 'Compare and contrast transcription and translation in Prokaryotes
More informationCISC 636 Computational Biology & Bioinformatics (Fall 2016)
CISC 636 Computational Biology & Bioinformatics (Fall 2016) Predicting Protein-Protein Interactions CISC636, F16, Lec22, Liao 1 Background Proteins do not function as isolated entities. Protein-Protein
More informationSUPPLEMENTARY 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 informationStructure to Function. Molecular Bioinformatics, X3, 2006
Structure to Function Molecular Bioinformatics, X3, 2006 Structural GeNOMICS Structural Genomics project aims at determination of 3D structures of all proteins: - organize known proteins into families
More informationRGP finder: prediction of Genomic Islands
Training courses on MicroScope platform RGP finder: prediction of Genomic Islands Dynamics of bacterial genomes Gene gain Horizontal gene transfer Gene loss Deletion of one or several genes Duplication
More informationSequence Alignment Techniques and Their Uses
Sequence Alignment Techniques and Their Uses Sarah Fiorentino Since rapid sequencing technology and whole genomes sequencing, the amount of sequence information has grown exponentially. With all of this
More informationSnoPatrol: How many snorna genes are there? Supplementary
SnoPatrol: How many snorna genes are there? Supplementary materials. Paul P. Gardner 1, Alex G. Bateman 1 and Anthony M. Poole 2,3 1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
More informationBIOLOGY CHAPTER ACTIVE READING GUIDE ANSWERS PDF
BIOLOGY CHAPTER ACTIVE READING GUIDE ANSWERS PDF ==> Download: BIOLOGY CHAPTER ACTIVE READING GUIDE ANSWERS PDF BIOLOGY CHAPTER ACTIVE READING GUIDE ANSWERS PDF - Are you searching for Biology Chapter
More information