GenBank. Direct submissions individual records (BankIt( BankIt,, Sequin) Batch submissions via (EST, GSS, STS) ftp accounts sequencing centers
|
|
|
- Jason Edwards
- 6 years ago
- Views:
Transcription
1
2 What is GenBank? NCBI s Primary Sequence Database Nucleotide sequence database Archival in nature GenBank Data Direct submissions individual records (BankIt( BankIt,, Sequin) Batch submissions via (EST, GSS, STS) ftp accounts sequencing centers Data shared nightly among three collaborating databases GenBank DNA Database of Japan (DDBJ). Mishima,, Japan European Molecular Biology Laboratory Database (EMBL) at EBI. Hinxton,, UK
3 The International Nucleotide Sequence Database Collaboration DDBJ/EMBL/GenBank NIH Entrez NCBI Submissions Updates GenBank DDBJ EMBL Data Library EMBL Submissions Updates CIB EBI NIG Submissions Updates SRS getentry
4 NCBI Homepage
5 NCBI Databases
6 NCBI Databases and Services GenBank largest sequence database Free public access to biomedical literature PubMed free Medline PubMed Central full text online access Entrez integrated molecular and literature databases BLAST highest volume sequence search service VAST structure similarity searches Software and Databases
7 LOCUS AY bp mrna linear PLN 04-MAY-2004 DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mrna, complete cds. ACCESSION AY VERSION AY GI: KEYWORDS. SOURCE Malus x domestica (cultivated apple) ORGANISM Malus x domestica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus. REFERENCE 1 (bases 1 to 1931) AUTHORS Pechous,S.W. and Whitaker,B.D. TITLE Cloning and functional expression of an (E,E)-alpha-farnesene synthase cdna from peel tissue of apple fruit JOURNAL Planta 219, (2004) REFERENCE 2 (bases 1 to 1931) AUTHORS Pechous,S.W. and Whitaker,B.D. TITLE Direct Submission JOURNAL Submitted (18-NOV-2002) PSI-Produce Quality and Safety Lab, USDA-ARS, Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD 20705, USA REFERENCE 3 (bases 1 to 1931) AUTHORS Pechous,S.W. and Whitaker,B.D. TITLE Direct Submission JOURNAL Submitted (25-JUN-2003) PSI-Produce Quality and Safety Lab, USDA-ARS, Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD 20705, USA REMARK Sequence update by submitter COMMENT On Jun 26, 2003 this sequence version replaced gi: FEATURES Location/Qualifiers source /organism="malus x domestica" /mol_type="mrna" /cultivar="'law Rome'" /db_xref="taxon:3750" /tissue_type="peel" gene /gene="afs1" CDS /gene="afs1" /note="terpene synthase" /codon_start=1 /product="(e,e)-alpha-farnesene synthase" /protein_id="aao " /db_xref="gi: " /translation="mefrvhlqadneqkifqnqmkpepeasylinqrrsanykpniwk NDFLDQSLISKYDGDEYRKLSEKLIEEVKIYISAETMDLVAKLELIDSVRKLGLANLF EKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQHGYKVSQDIFGRFMDEKGTLE DFLHKNEDLLYNISLIVRLNNDLGTSAAEQERGDSPSSIVCYMREVNASEETARKNIK GMIDNAWKKVNGKCFTTNQVPFLSSFMNNATNMARVAHSLYKDGDGFGDQEKGPRTHI LSLLFQPLVN" ORIGIN 1 ttcttgtatc ccaaacatct cgagcttctt gtacaccaaa ttaggtattc actatggaat 61 tcagagttca cttgcaagct gataatgagc agaaaatttt tcaaaaccag atgaaacccg 121 aacctgaagc ctcttacttg attaatcaaa gacggtctgc aaattacaag ccaaatattt 181 ggaagaacga tttcctagat caatctctta tcagcaaata cgatggagat gagtatcgga 241 agctgtctga gaagttaata gaagaagtta agatttatat atctgctgaa acaatggatt // A Traditional GenBank Record Header The Flatfile Format Feature Table Sequence
8 Traditional GenBank Record ACCESSION U07418 VERSION U GI: Accession Stable Stable Reportable Universal Version Tracks Tracks changes in in sequence GI GI number NCBI NCBI internal internal use use well annotated well annotated the sequence is the data the sequence is the data
9 Sequence and Database Identifiers Locus, accession, gi,, version Locus Name Sequence length mol-type mrna (= cdna) rrna snrna DNA GB Division Modification Date LOCUS AF bp mrna INV 02-MAR-2000 DEFINITION Limulus polyphemus myosin III mrna, complete cds. ACCESSION AF VERSION AF GI: Accession Number DEF line (Title) Accession.version gi number
10 Sequence Indicates beginning of sequence data BASE COUNT 1201 a 689 c 782 g 1136 t ORIGIN 1 tcgacatctg tggtcgcttt ttttagtaat aaaaaattgt attatgacgt cctatctgtt <sequence omitted> 3721 accaatgtta taatatgaaa tgaaataaag cagtcatggt agcagtggct gtttgaaata 3781 aagatacagt aactagggaa aaaaaaaa // End of record
11 Using Entrez An integrated database search and retrieval system
12 WWW Access Entrez & BLAST
13 Entrez: : Neighboring and Hard Links Word weight PubMed abstracts Phylogeny Taxonomy Genomes 3 3-D Structure (MMDB) VAST BLAST Nucleotide sequences Protein sequences BLAST
14 WWW Entrez All of MEDLINE plus others Abstracts Links to online Journals GenBank, EMBL, DDBJ RefSeq, PDB GenBank, DDBJ, EMBL translations PDB, PIR, SWISS-PROT, PRF, RefSeq NCBI s MMDB - derived from PDB Graphical views Assembled sequence and mapping data Population and phylogenetic studies MIM Now in Entrez NCBI s Taxonomy Hierarchical tree structure access to sequences
15 Entrez Nucleotides Mouse
![Document Summaries: Mouse[All Fields]](/docs-images/75/72573276/images/16-1.jpg "3 million records Chicken not mouse!?")
16 Document Summaries: Mouse[All Fields] 3 million records Chicken not mouse!?
17 Entrez Nucleotides: Limits: Preview/Index Mouse
18 Accession All Fields Author Name EC/RN Number Feature key Filter Gene Name Issue Journal Name Keyword Modification Date Organism Page Number Primary Accession Properties Protein Name Publication Date SeqID String Sequence Length Substance Name Text Word Title Word Uid Volume Entrez Nucleotides: Limits Mouse Field Restriction Exclude unwanted categories of sequences Molecule Genomic DNA/RNA mrna rrna Only From RefSeq GenBank EMBL DDBJ Gene Location Genomic DNA/RNA Mitochondrion Chloroplast
19 Entrez Nucleotides: Limits: Organism Mouse
![Document Summaries: Mouse[Organism]](/docs-images/75/72573276/images/20-1.jpg "2,976,070[All Fields] -2,921,009[Organism]")
20 Document Summaries: Mouse[Organism] 2,976,070[All Fields] -2,921,009[Organism] 55,061
21 Exclude Bulk Sequences, mrna
22 Adding Terms: Preview/Index Accession All Fields Author Name EC/RN Number Feature key Filter Gene Name Issue Journal Name Keyword Modification Date Organism Page Number Primary Accession Properties Search History Protein glyceraldehyde Name 3 phosphate dehydrogenase Publication Date SeqID String Sequence Length Substance Name Text Word Title Word Uid Volume
23 Mouse GAPD Records (("Mus musculus"[organism] AND glyceraldehyde 3 phosphate dehydrogenase[title Word]) AND ((((((1900[MDAT] : 3000[MDAT]) NOT gbdiv_est[prop]) NOT gbdiv_sts[prop]) NOT gbdiv_gss[prop]) NOT gbdiv_htg[prop]) NOT gbdiv_pat[prop])) AND biomol_mrna[prop] Properties Field Terms
24 Displaying Mouse GAPD Records Links and neighbors (related records) Summary Brief GenBank Formats ASN.1 FASTA GI list LinkOut PubMed Links Protein Links Nucleotide Neighbors PopSet Links Structure Links Genome Links Taxonomy Links OMIM Links
25 FASTA Format FASTA Definition Line >gi gb M MUSGAPDS Mus musculus testis-specific isoform of glycerald GGCAGCCAGGCCATGAGATCTTAGGCCATGTCGAGACGTGACGTGGTCCTTACCAATGTTACTGTTGTCC AGCTACGGCGGGACCGATGCCCATGCCCATGCCCATGCCCATGTCCATGCCCATGCCCTGTGATCAGACC >gi gb M MUSGAPDS ACCTCCACCCAAGCTTGAGGATCCACCACCCACGGTTGAAGAACAGCCACCGCCACCGCCGCCGCCACCT > CCACCTCCACCACCACCTCCTCCTCCTCCTCCACCCCAGATAGAGCCAGACAAGTTTGAAGAGGCTCCCC CTCCCCCTCCCCCTCCTCCTCCTCCTCCCCCTCCCCCTCCTCCACCACTCCAAAAGCCAGCTAGAGAGCT GACAGTGGGTATCAATGGATTTGGACGCATTGGTCGTCTGGTGCTGCGAGTCTGCATGGAGAAGGGCATT AGGGTGGTAGCAGTGAATGACCCATTCATTGATCCAGAATACATGGTTTACATGTTCAAATATGACTCCA gi number CACATGGTAGATACAAAGGAAACGTGGAACATAAGAATGGACAACTAGTTGTGGACAACCTTGAGATCAA CACGTACCAGTGCAAAGACCCTAAAGAAATCCCCTGGAGCTCTATAGGGAATCCCTACGTGGTGGAGTGT ACAGGCGTCTATCTGTCCATCGAGGCAGCTTCGGCACATATTTCATCTGGTGCCAGGCGTGTGGTGGTCA CTGCACCCTCCCCCGATGCACCCATGTTTGTCATGGGAGTGAACGAGAAGGACTATAACCCTGGCTCTAT Accession number Database Identifiers GACCATTGTCAGCAATGCATCCTGTACCACCAACTGCCTGGCTCCTCTCGCCAAGGTTATTCATGAAAAC TTCGGGATCGTGGAAGGGCTAATGACCACAGTCCATTCCTACACAGCCACTCAGAAGACAGTGGATGGGC gb GenBank CATCAAAGAAGGACTGGCGAGGTGGCCGCGGCGCTCACCAAAACATCATCCCATCGTCCACTGGGGCTGC emb EMBL CAAGGCTGTAGGCAAAGTCATCCCAGAGCTCAAAGGGAAGCTAACAGGAATGGCATTCCGGGTGCCAACC dbj DDBJ CCAAACGTGTCAGTTGTGGACCTGACCTGCCGCCTGGCCAAGCCTGCTTCTTACTCGGCTATCACGGAGG CTGTGAAAGCTGCAGCCAAGGGACCTTTGGCTGGCATCCTTGCTTACACAGAGGACCAGGTGGTCTCCAC sp SWISS-PROT GGACTTTAACGGCAATCCCCATTCTTCCATCTTTGATGCTAAGGCTGGAATTGCCCTCAATGACAACTTC pdb Protein Databank GTGAAGCTTGTTGCCTGGTACGACAACGAATATGGCTACAGTAACCGAGTGGTCGACCTCCTCCGCTACA pir PIR TGTTTAGCCGAGAGAAGTAACACAAAAGGCCCCTCCTTGCTCCCCTGCGCACCTCGCGTTCCTGACTTCG GCTTCCACTCAAAGGCGCCGCCACCGGGTCAACAATGAAATAAAAACGAGAATGCGC prf PRF ref RefSeq Locus Name
26 Break! 5 minutes
National Center for Biotechnology Information (NCBI):
National Center for Biotechnology Information (NCBI): http://www.ncbi.nlm.nih.gov By: Dr Hadi Mozafari As a national resource for molecular biology information, NCBI's mission is to develop new information
NCBI Molecular Biology Resources. NCBI Resources
NBI Molecular Biology Resources A Field Guide NBI Resources The NBI Entrez System NBI Sequence Databases Primary data: GenBank Derivative data: RefSeq, Gene Protein Structure and Function Sequence polymorphisms
A Field Guide to GenBank and NCBI Molecular Biology Resources
A Field Guide to GenBank and NCBI Molecular Biology Resources slightly modified from Peter Cooper ftp://ftp.ncbi.nih.gov/pub/cooper/fieldguide/ Eric Sayers ftp://ftp.ncbi.nih.gov/pub/sayers/field_guide/u_penn/
Types of Databases - By Scope
Biological Databases Bioinformatics Workshop 2009 Chi-Cheng Lin, Ph.D. Department of Computer Science Winona State University clin@winona.edu Biological Databases Data Domains - By Scope - By Level of
ELE4120 Bioinformatics. Tutorial 5
ELE4120 Bioinformatics Tutorial 5 1 1. Database Content GenBank RefSeq TPA UniProt 2. Database Searches 2 Databases A common situation for alignment is to search through a database to retrieve the similar
Computational Biology and Bioinformatics
Computational Biology and Bioinformatics Computational biology Development of algorithms to solve problems in biology Bioinformatics Application of computational biology to the analysis and management
What You NEED to Know
What You NEED to Know Major DNA Databases NCBI RefSeq EBI DDBJ Protein Structural Databases PDB SCOP CCDC Major Protein Sequence Databases UniprotKB Swissprot PIR TrEMBL Genpept Other Major Databases MIM
Databases NCBI - ENTREZ
Databases NCBI - ENTREZ Data & Software Resources BLAST CDD COG GENSAT GenBank Whole Genome Shotgun Sequences Gene Gene Expression Nervous System Atlas (GENSAT) Gene Expression Omnibus (GEO) Profiles
NCBI Molecular Biology Resources. Entrez & BLAST. Entrez: Database Integration. Database Searching with Entrez. WWW Access. Using Entrez.
NCBI Molecular Biology Resources Using Entrez WWW Access Entrez & BLAST March 2007 Phylogeny Entrez: Database Integration Taxonomy PubMed abstracts Genomes Word weight 3-D Structure VAST Neighbors Related
Introduction to BIOINFORMATICS
Introduction to BIOINFORMATICS Antonella Lisa CABGen Centro di Analisi Bioinformatica per la Genomica Tel. 0382-546361 E-mail: lisa@igm.cnr.it http://www.igm.cnr.it/pagine-personali/lisa-antonella/ What
NCBI web resources I: databases and Entrez
NCBI web resources I: databases and Entrez Yanbin Yin Most materials are downloaded from ftp://ftp.ncbi.nih.gov/pub/education/ 1 Homework assignment 1 Two parts: Extract the gene IDs reported in table
Protein Bioinformatics Part I: Access to information
Protein Bioinformatics Part I: Access to information 260.655 April 6, 2006 Jonathan Pevsner, Ph.D. pevsner@kennedykrieger.org Outline [1] Proteins at NCBI RefSeq accession numbers Cn3D to visualize structures
Redundancy at GenBank => RefSeq. RefSeq vs GenBank. Databases, cont. Genome sequencing using a shotgun approach. Sequenced eukaryotic genomes
Databases, cont. Redundancy at GenBank => RefSeq http://www.ncbi.nlm.nih.gov/books/bv.fcg i?rid=handbook RefSeq vs GenBank Many sequences are represented more than once in GenBank 2003 RefSeq collection
Introduction to Bioinformatics CPSC 265. What is bioinformatics? Textbooks
Introduction to Bioinformatics CPSC 265 Thanks to Jonathan Pevsner, Ph.D. Textbooks Johnathan Pevsner, who I stole most of these slides from (thanks!) has written a textbook, Bioinformatics and Functional
EECS 730 Introduction to Bioinformatics Sequence Alignment. Luke Huan Electrical Engineering and Computer Science
EECS 730 Introduction to Bioinformatics Sequence Alignment Luke Huan Electrical Engineering and Computer Science http://people.eecs.ku.edu/~jhuan/ Database What is database An organized set of data Can
Chapter 2: Access to Information
Chapter 2: Access to Information Outline Introduction to biological databases Centralized databases store DNA sequences Contents of DNA, RNA, and protein databases Central bioinformatics resources: NCBI
Introduction to Molecular Biology Databases
Introduction to Molecular Biology Databases Laboratorio de Bioinformática Centro de Astrobiología INTA-CSIC Centro de Astrobiología PRESENT BIOLOGY RESEARCH Data sources Genome sequencing projects: genome
This software/database/presentation is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part
This software/database/presentation is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the author's official duties as a United States Government
GenBank. Dennis A. Benson*, Mark S. Boguski, David J. Lipman, James Ostell and B. F. Francis Ouellette
1998 Oxford University Press Nucleic Acids Research, 1998, Vol. 26, No. 1 1 7 GenBank Dennis A. Benson*, Mark S. Boguski, David J. Lipman, James Ostell and B. F. Francis Ouellette National Center for Biotechnology
The University of California, Santa Cruz (UCSC) Genome Browser
The University of California, Santa Cruz (UCSC) Genome Browser There are hundreds of available userselected tracks in categories such as mapping and sequencing, phenotype and disease associations, genes,
Gene-centered resources at NCBI
COURSE OF BIOINFORMATICS a.a. 2014-2015 Gene-centered resources at NCBI We searched Accession Number: M60495 AT NCBI Nucleotide Gene has been implemented at NCBI to organize information about genes, serving
I nternet Resources for Bioinformatics Data and Tools
~i;;;;;;;'s :.. ~,;;%.: ;!,;s163 ~. s :s163:: ~s ;'.:'. 3;3 ~,: S;I:;~.3;3'/////, IS~I'//. i: ~s '/, Z I;~;I; :;;; :;I~Z;I~,;'//.;;;;;I'/,;:, :;:;/,;'L;;;~;'~;~,::,:, Z'LZ:..;;',;';4...;,;',~/,~:...;/,;:'.::.
Bioinformatics for Proteomics. Ann Loraine
Bioinformatics for Proteomics Ann Loraine aloraine@uab.edu What is bioinformatics? The science of collecting, processing, organizing, storing, analyzing, and mining biological information, especially data
Two Mark question and Answers
1. Define Bioinformatics Two Mark question and Answers Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline. There are three
Compiled by Mr. Nitin Swamy Asst. Prof. Department of Biotechnology
Bioinformatics Model Answers Compiled by Mr. Nitin Swamy Asst. Prof. Department of Biotechnology Page 1 of 15 Previous years questions asked. 1. Describe the software used in bioinformatics 2. Name four
AAGTGCCACTGCATAAATGACCATGAGTGGGCACCGGTAAGGGAGGGTGATGCTATCTGGTCTGAAG. Protein 3D structure. sequence. primary. Interactions Mutations
Introduction to Databases Lecture Outline Shifra Ben-Dor Irit Orr Introduction Data and Database types Database components Data Formats Sample databases How to text search databases What units of information
Biological databases an introduction
Biological databases an introduction By Dr. Erik Bongcam-Rudloff SLU 2017 Biological Databases Sequence Databases Genome Databases Structure Databases Sequence Databases The sequence databases are the
7.91 Lecture #1 Introduction to Bioinformatics
7.91 Lecture #1 Introduction to Bioinformatics Focus on Kinases Michael Yaffe & Pairwise Sequence Comparisons ARDFSHGLLENKLLGCDSMRWE.::..:::..:::: :::. GRDYKMALLEQWILGCD-MRWD Reading: This lecture: Mount
Databases in genomics
Databases in genomics Search in biological databases: The most common task of molecular biologist researcher, to answer to the following ques7ons:! Are they new sequences deposited in biological databases
Genome Resources. Genome Resources. Maj Gen (R) Suhaib Ahmed, HI (M)
Maj Gen (R) Suhaib Ahmed, I (M) The human genome comprises DNA sequences mostly contained in the nucleus. A small portion is also present in the mitochondria. The nuclear DNA is present in chromosomes.
Introduction to Bioinformatics
Introduction to Bioinformatics 260.602.01 September 1, 2006 Jonathan Pevsner, Ph.D. pevsner@kennedykrieger.org Teaching assistants Hugh Cahill (hugh@jhu.edu) Jennifer Turney (jturney@jhsph.edu) Meg Zupancic
Introduction and Public Sequence Databases. BME 110/BIOL 181 CompBio Tools
Introduction and Public Sequence Databases BME 110/BIOL 181 CompBio Tools Todd Lowe March 29, 2011 Course Syllabus: Admin http://www.soe.ucsc.edu/classes/bme110/spring11 Reading: Chapters 1, 2 (pp.29-56),
Entrez Gene: gene-centered information at NCBI
D54 D58 Nucleic Acids Research, 2005, Vol. 33, Database issue doi:10.1093/nar/gki031 Entrez Gene: gene-centered information at NCBI Donna Maglott*, Jim Ostell, Kim D. Pruitt and Tatiana Tatusova National
NUCLEIC ACIDS. DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid): information storage molecules made up of nucleotides.
NUCLEIC ACIDS DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid): information storage molecules made up of nucleotides. Base Adenine Guanine Cytosine Uracil Thymine Abbreviation A G C U T DNA RNA 2
Biological databases an introduction
Biological databases an introduction By Dr. Erik Bongcam-Rudloff SGBC-SLU 2016 VALIDATION Experimental Literature Manual or semi-automatic computational analysis EXPERIMENTAL Costs Needs skilled manpower
Outline. Evolution. Adaptive convergence. Common similarity problems. Chapter 7: Similarity searches on sequence databases
Chapter 7: Similarity searches on sequence databases All science is either physics or stamp collection. Ernest Rutherford Outline Why is similarity important BLAST Protein and DNA Interpreting BLAST Individualizing
BIOINF525: INTRODUCTION TO BIOINFORMATICS LAB SESSION 1
BIOINF525: INTRODUCTION TO BIOINFORMATICS LAB SESSION 1 Bioinformatics Databases http://bioboot.github.io/bioinf525_w17/module1/#1.1 Dr. Barry Grant Jan 2017 Overview: The purpose of this lab session is
NCBI Molecular Biology Resources
NCBI Molecular Biology Resources Part 2: Using NCBI BLAST December 2009 Using BLAST Basics of using NCBI BLAST Using the new Interface Improved organism and filter options New Services Primer BLAST Align
Sequence Databases. Chapter 2. caister.com/bioinformaticsbooks. Paul Rangel. Sequence Databases
Chapter 2 Paul Rangel Abstract DNA and Protein sequence databases are the cornerstone of bioinformatics research. DNA databases such as GenBank and EMBL accept genome data from sequencing projects around
Bioinformatics for Cell Biologists
Bioinformatics for Cell Biologists 15 19 March 2010 Developmental Biology and Regnerative Medicine (DBRM) Schedule Monday, March 15 09.00 11.00 Introduction to course and Bioinformatics (L1) D224 Helena
Integration of data management and analysis for genome research
Integration of data management and analysis for genome research Volker Brendel Deparment of Zoology & Genetics and Department of Statistics Iowa State University 2112 Molecular Biology Building Ames, Iowa
Introduction on Several Popular Nucleic Acids Databases
Introduction on Several Popular Nucleic Acids Databases Changmin Liao Library, China West Normal University, Nanchong City, P. R. liaochangminlxh@yahoo.com.cn Abstract-Nucleic acids are major biological
Data Retrieval from GenBank
Data Retrieval from GenBank Peter J. Myler Bioinformatics of Intracellular Pathogens JNU, Feb 7-0, 2009 http://www.ncbi.nlm.nih.gov (January, 2007) http://ncbi.nlm.nih.gov/sitemap/resourceguide.html Accessing
Applied Bioinformatics
Applied Bioinformatics Bing Zhang Department of Biomedical Informatics Vanderbilt University bing.zhang@vanderbilt.edu Course overview What is bioinformatics Data driven science: the creation and advancement
B I O I N F O R M A T I C S
B I O I N F O R M A T I C S Kristel Van Steen, PhD 2 Montefiore Institute - Systems and Modeling GIGA - Bioinformatics ULg kristel.vansteen@ulg.ac.be SUPPLEMENTARY CHAPTER: DATA BASES AND MINING 1 What
Databases in Bioinformatics. Molecular Databases. Molecular Databases. NCBI Databases. BINF 630: Bioinformatics Methods
Databases in Bioinformatics BINF 630: Bioinformatics Methods Iosif Vaisman Email: ivaisman@gmu.edu Molecular Databases Molecular Databases Nucleic acid sequences: GenBank, DNA Data Bank of Japan, EMBL
Bioinformatics Prof. M. Michael Gromiha Department of Biotechnology Indian Institute of Technology, Madras. Lecture - 5a Protein sequence databases
Bioinformatics Prof. M. Michael Gromiha Department of Biotechnology Indian Institute of Technology, Madras Lecture - 5a Protein sequence databases In this lecture, we will mainly discuss on Protein Sequence
Introduction to Bioinformatics. What are the goals of the course? Who is taking this course? Textbook. Web sites. Literature references
Introduction to Bioinformatics Who is taking this course? People with very diverse backgrounds in biology Some people with backgrounds in computer science and biostatistics Most people (will) have a favorite
Why Use BLAST? David Form - August 15,
Wolbachia Workshop 2017 Bioinformatics BLAST Basic Local Alignment Search Tool Finding Model Organisms for Study of Disease Can yeast be used as a model organism to study cystic fibrosis? BLAST Why Use
Introduc)on to Databases and Resources Biological Databases and Resources
Introduc)on to Bioinforma)cs Online Course : IBT Introduc)on to Databases and Resources Biological Databases and Resources Learning Objec)ves Introduc)on to Databases and Resources - Understand how bioinforma)cs
MOLECULAR BIOLOGY DATABASES. Juan Carlos Sánchez Ferrero
MOLECULAR BIOLOGY DATABASES Juan Carlos Sánchez Ferrero Centro Nacional de Biotecnología, CSIC July 2008 GROWING NUMBER OF DATA Molecular biology data explosion in the omics era: genome sequencing, high-throughput
AP BIOLOGY. Investigation #3 Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST. Slide 1 / 32. Slide 2 / 32.
New Jersey Center for Teaching and Learning Slide 1 / 32 Progressive Science Initiative This material is made freely available at www.njctl.org and is intended for the non-commercial use of students and
Basic Bioinformatics: Homology, Sequence Alignment,
Basic Bioinformatics: Homology, Sequence Alignment, and BLAST William S. Sanders Institute for Genomics, Biocomputing, and Biotechnology (IGBB) High Performance Computing Collaboratory (HPC 2 ) Mississippi
Sequence Databases and database scanning
Sequence Databases and database scanning Marjolein Thunnissen Lund, 2012 Types of databases: Primary sequence databases (proteins and nucleic acids). Composite protein sequence databases. Secondary databases.
Linking the EMBL Australia Bioinformatics Resource with the Australian National Data Service
Linking the EMBL Australia Bioinformatics Resource with the Australian National Data Service JEFF CHRISTIANSEN ANDS PIERRE CHAUMEIL - QFAB DOMINIQUE GORSE QFAB MARK RAGAN IMB/UQ EMBL Australia Australia
NATIONAL OPEN UNIVERSITY OF NIGERIA SCHOOL OF ARTS AND SOCIAL SCIENCES COURSE CODE: BIO 316 COURSE TITLE: INTRODUCTION TO BIOINFORMATICS
NATIONAL OPEN UNIVERSITY OF NIGERIA SCHOOL OF ARTS AND SOCIAL SCIENCES COURSE CODE: BIO 316 COURSE TITLE: INTRODUCTION TO BIOINFORMATICS 1 Course Code : BIO 316 Course Title : Introduction to Bioinformatics
NiceProt View of Swiss-Prot: P18907
Hosted by NCSC US ExPASy Home page Site Map Search ExPASy Contact us Swiss-Prot Mirror sites: Australia Bolivia Canada China Korea Switzerland Taiwan Search Swiss-Prot/TrEMBL for horse alpha Go Clear NiceProt
Bioinformatics overview
Bioinformatics overview Aplicações biomédicas em plataformas computacionais de alto desempenho Aplicaciones biomédicas sobre plataformas gráficas de altas prestaciones Biomedical applications in High performance
Why learn sequence database searching? Searching Molecular Databases with BLAST
Why learn sequence database searching? Searching Molecular Databases with BLAST What have I cloned? Is this really!my gene"? Basic Local Alignment Search Tool How BLAST works Interpreting search results
Bioinformatics Databases
Bioinformatics Databases Dr. Taysir Hassan Abdel Hamid Lecturer, Information Systems Department Faculty of Computer and Information Assiut University taysirhs@aun.edu.eg taysir_soliman@hotmail.com Agenda
From AP investigative Laboratory Manual 1
Comparing DNA Sequences to Understand Evolutionary Relationships. How can bioinformatics be used as a tool to determine evolutionary relationships and to better understand genetic diseases? BACKGROUND
ONLINE BIOINFORMATICS RESOURCES
Dedan Githae Email: d.githae@cgiar.org BecA-ILRI Hub; Nairobi, Kenya 16 May, 2014 ONLINE BIOINFORMATICS RESOURCES Introduction to Molecular Biology and Bioinformatics (IMBB) 2014 The larger picture.. Lower
Will discuss proteins in view of Sequence (I,II) Structure (III) Function (IV) proteins in practice
Will discuss proteins in view of Sequence (I,II) Structure (III) Function (IV) proteins in practice integration - web system (V) 1 Touring the Protein Space (outline) 1. Protein Sequence - how rich? How
Lecture 2 Introduction to Data Formats
Introduction to Bioinformatics for Medical Research Gideon Greenspan gdg@cs.technion.ac.il Lecture 2 Introduction to Data Formats Introduction to Data Formats Real world, data and formats Sequences and
Chapter 2. Genomic Databases and Resources at the National Center for Biotechnology Information. Tatiana Tatusova. Abstract. 1.
Chapter 2 Genomic Databases and Resources at the National Center for Biotechnology Information Tatiana Tatusova Abstract The National Center for Biotechnology Information (NCBI), as a primary public repository
Genome and DNA Sequence Databases. BME 110: CompBio Tools Todd Lowe April 5, 2007
Genome and DNA Sequence Databases BME 110: CompBio Tools Todd Lowe April 5, 2007 Admin Reading: Chapters 2 & 3 Notes available in PDF format on-line (see class calendar page): http://www.soe.ucsc.edu/classes/bme110/spring07/bme110-calendar.html
SeattleSNPs Interactive Tutorial: Database Inteface Entrez, dbsnp, HapMap, Perlegen
SeattleSNPs Interactive Tutorial: Database Inteface Entrez, dbsnp, HapMap, Perlegen The tutorial is designed to take you through the steps necessary to access SNP data from the primary database resources:
DNAFSMiner: A Web-Based Software Toolbox to Recognize Two Types of Functional Sites in DNA Sequences
DNAFSMiner: A Web-Based Software Toolbox to Recognize Two Types of Functional Sites in DNA Sequences Huiqing Liu Hao Han Jinyan Li Limsoon Wong Institute for Infocomm Research, 21 Heng Mui Keng Terrace,
Databases/Resources on the web
Databases/Resources on the web Jon K. Lærdahl jonkl@medisin.uio.no A lot of biological databases available on the web... MetaBase, the database of biological databases (1801 entries) - h p://metadatabase.org
Following text taken from Suresh Kumar. Bioinformatics Web - Comprehensive educational resource on Bioinformatics. 6th May.2005
Bioinformatics is the recording, annotation, storage, analysis, and searching/retrieval of nucleic acid sequence (genes and RNAs), protein sequence and structural information. This includes databases of
Bioinformatics Tools. Stuart M. Brown, Ph.D Dept of Cell Biology NYU School of Medicine
Bioinformatics Tools Stuart M. Brown, Ph.D Dept of Cell Biology NYU School of Medicine Bioinformatics Tools Stuart M. Brown, Ph.D Dept of Cell Biology NYU School of Medicine Overview This lecture will
A Prac'cal Guide to NCBI BLAST
A Prac'cal Guide to NCBI BLAST Leonardo Mariño-Ramírez NCBI, NIH Bethesda, USA June 2018 1 NCBI Search Services and Tools Entrez integrated literature and molecular databases Viewers BLink protein similarities
Bioinformatics for Molecular Biology
Bioinformatics for Molecular Biology Databases & Accessing data Today s Programme Biological databases Brief introduction What is UNIX? Why should you learn UNIX? Bioinformatics Core Facility Setting up
Basic molecular biology and overview of major bioinforma6cs web resources. Yanbin Yin Fall 2015
Basic molecular biology and overview of major bioinforma6cs web resources Yanbin Yin Fall 2015 1 Outline Basic molecular biology Web Databases Web Servers 2 References NAR database and web server annual
CBRS Chlamydiae community re-annotation
CBRS Chlamydiae community re-annotation Session schedule Intro and automatic annotation (T. Weinmaier) Nomenclature Manual refinement Submission / Publication Session schedule Intro and automatic annotation
Introduction to Bioinformatics for Medical Research. Gideon Greenspan TA: Oleg Rokhlenko. Lecture 1
Introduction to Bioinformatics for Medical Research Gideon Greenspan gdg@cs.technion.ac.il TA: Oleg Rokhlenko Lecture 1 Introduction to Bioinformatics Introduction to Bioinformatics What is Bioinformatics?
Agenda. Web Databases for Drosophila. Gene annotation workflow. GEP Drosophila annotation projects 01/01/2018. Annotation adding labels to a sequence
Agenda GEP annotation project overview Web Databases for Drosophila An introduction to web tools, databases and NCBI BLAST Web databases for Drosophila annotation UCSC Genome Browser NCBI / BLAST FlyBase
Access to Information from Molecular Biology and Genome Research
Future Needs for Research Infrastructures in Biomedical Sciences Access to Information from Molecular Biology and Genome Research DG Research: Brussels March 2005 User Community for this information is
Genome 559 Intro to Statistical and Computational Genomics Lecture 19b: Biopython Larry Ruzzo (Thanks again to Mary Kuhner for many slides)
Genome 559 Intro to Statistical and Computational Genomics 2009 Lecture 19b: Biopython Larry Ruzzo (Thanks again to Mary Kuhner for many slides) 1 1 Minute Responses biopython makes me appreciate python
user s guide Question 3
Question 3 During a positional cloning project aimed at finding a human disease gene, linkage data have been obtained suggesting that the gene of interest lies between two sequence-tagged site markers.
G4120: Introduction to Computational Biology
G4120: Introduction to Computational Biology Oliver Jovanovic, Ph.D. Columbia University Department of Microbiology Lecture 3 February 13, 2003 Copyright 2003 Oliver Jovanovic, All Rights Reserved. Bioinformatics
FACULTY OF BIOCHEMISTRY AND MOLECULAR MEDICINE
FACULTY OF BIOCHEMISTRY AND MOLECULAR MEDICINE BIOMOLECULES COURSE: COMPUTER PRACTICAL 1 Author of the exercise: Prof. Lloyd Ruddock Edited by Dr. Leila Tajedin 2017-2018 Assistant: Leila Tajedin (leila.tajedin@oulu.fi)
Since 2002 a merger and collaboration of three databases: Swiss-Prot & TrEMBL
Since 2002 a merger and collaboration of three databases: Swiss-Prot & TrEMBL PIR-PSD Funded mainly by NIH (US) to be the highest quality, most thoroughly annotated protein sequence database o A high quality
The human gene encoding Glucose-6-phosphate dehydrogenase (G6PD) is located on chromosome X in cytogenetic band q28.
Data mining in Ensembl with BioMart Worked Example The human gene encoding Glucose-6-phosphate dehydrogenase (G6PD) is located on chromosome X in cytogenetic band q28. Which other genes related to human
BIOINFORMATICS FOR DUMMIES MB&C2017 WORKSHOP
Jasper Decuyper BIOINFORMATICS FOR DUMMIES MB&C2017 WORKSHOP MB&C2017 Workshop Bioinformatics for dummies 2 INTRODUCTION Imagine your workspace without the computers Both in research laboratories and in
Array-Ready Oligo Set for the Rat Genome Version 3.0
Array-Ready Oligo Set for the Rat Genome Version 3.0 We are pleased to announce Version 3.0 of the Rat Genome Oligo Set containing 26,962 longmer probes representing 22,012 genes and 27,044 gene transcripts.
BLASTing through the kingdom of life
Information for teachers Description: In this activity, students copy unknown DNA sequences and use them to search GenBank, the main database of nucleotide sequences at the National Center for Biotechnology
Retrieval of gene information at NCBI
Retrieval of gene information at NCBI Some notes 1. http://www.cs.ucf.edu/~xiaoman/fall/ 2. Slides are for presenting the main paper, should minimize the copy and paste from the paper, should write in
Evolutionary Genetics. LV Lecture with exercises 6KP. Databases
Evolutionary Genetics LV 25600-01 Lecture with exercises 6KP Databases HS2018 Bioinformatics - R R Assignment The Minimalistic Approach!2 Bioinformatics - R Possible Exam Questions for R: Q1: The function
MS bioinformatics analysis for proteomics. Protein anotations
MS bioinformatics analysis for proteomics Protein anotations UCO - Córdoba Organized by: ProteoRed, EUPA and Seprot Alberto Medina January, 23rd 2009 Summary Introduction Some issues Software: Fatigo -
Gene-centered databases and Genome Browsers
COURSE OF BIOINFORMATICS a.a. 2015-2016 Gene-centered databases and Genome Browsers We searched Accession Number: M60495 AT NCBI Nucleotide Gene has been implemented at NCBI to organize information about
Gene-centered databases and Genome Browsers
COURSE OF BIOINFORMATICS a.a. 2016-2017 Gene-centered databases and Genome Browsers We searched Accession Number: M60495 AT NCBI Nucleotide Gene has been implemented at NCBI to organize information about
Leonardo Mariño-Ramírez, PhD NCBI / NLM / NIH. BIOL 7210 A Computational Genomics 2/18/2015
Leonardo Mariño-Ramírez, PhD NCBI / NLM / NIH BIOL 7210 A Computational Genomics 2/18/2015 The $1,000 genome is here! http://www.illumina.com/systems/hiseq-x-sequencing-system.ilmn Bioinformatics bottleneck
Making Sense of DNA and Protein Sequences. Lily Wang, PhD Department of Biostatistics Vanderbilt University
Making Sense of DNA and Protein Sequences Lily Wang, PhD Department of Biostatistics Vanderbilt University 1 Outline Biological background Major biological sequence databanks Basic concepts in sequence
Discover the Microbes Within: The Wolbachia Project. Bioinformatics Lab
Bioinformatics Lab ACTIVITY AT A GLANCE "Understanding nature's mute but elegant language of living cells is the quest of modern molecular biology. From an alphabet of only four letters representing the
ab initio and Evidence-Based Gene Finding
ab initio and Evidence-Based Gene Finding A basic introduction to annotation Outline What is annotation? ab initio gene finding Genome databases on the web Basics of the UCSC browser Evidence-based gene
Worksheet for Bioinformatics
Worksheet for Bioinformatics ACTIVITY: Learn to use biological databases and sequence analysis tools Exercise 1 Biological Databases Objective: To use public biological databases to search for latest research
Computational Molecular Biology Intro. Alexander (Sacha) Gultyaev
Computational Molecular Biology Intro Alexander (Sacha) Gultyaev a.p.goultiaev@liacs.leidenuniv.nl Biopolymer sequences DNA: double-helical nucleic acid. Monomers: nucleotides C, A, T, G. RNA: (single-stranded)
Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell and Eric W. Sayers*
D32 D37 Nucleic Acids Research, 2011, Vol. 39, Database issue Published online 10 November 2010 doi:10.1093/nar/gkq1079 GenBank Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell and
Bioinformatics Blue Print of Genes. Prof. Fatchiyah, M.Kes. Ph.D Dept. of Biology School of Math. and Natural Sciences Brawijaya University
Bioinformatics Blue Print of Genes Prof. Fatchiyah, M.Kes. Ph.D Dept. of Biology School of Math. and Natural Sciences Brawijaya University What is Bioinformatics The use of computers to collect, analyze,