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lect12-5011

Course: BINF 5011, Fall 2009
School: University of Medicine...
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A 1 2 Database database (or database system) is formally composed of three components: 1) data in a searchable form 2) a generic search engine 3) a query language appropriate to the domain of the data. Chemical Databases Chemical Database Chemical Databases are databases containing encoded chemical structures along with molecular and atomic data. Lecture 12 UMDNJ - School of Health Related Professions...

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A 1 2 Database database (or database system) is formally composed of three components: 1) data in a searchable form 2) a generic search engine 3) a query language appropriate to the domain of the data. Chemical Databases Chemical Database Chemical Databases are databases containing encoded chemical structures along with molecular and atomic data. Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 3 4 Bioinformatics Database Bioinformatics Databases A) Sequence Database Nucleic Acids (NCBI:GenBank) Proteins Bioinformatics Database Bioinformatics Databases C) Others Not Sequence Nor Structure B) Structure Database Nucleic Acids (Nucleic Acid Database) Proteins (Protein Data Bank) Small Molecules (Cambridge Structural Database) Chemical Database Lecture 12 UMDNJ - School of Health Related Professions Resources Nucleic Acids Research 1 st Issue Every Year BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 5 6 Databases What is not a database? Not all high quality collections of structural data is database if they do not satisfy the above condition. Brookhaven Protein Data Bank New PDB at RCSB is Databases Primary vs Secondary Databases. Primary - Original Data Secondary Annotation on the Primary Data Value added Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 1 7 8 Primary Sequence Databases Primary Sequence Databases (contd.) Entrez GenBank GenBank (143.0) NCBI at NIH 8/15/04 41,808,045,653 base 37,343,937 sequence Database Search DDBJ EMBL DDBJ DNA Databank of Japan Lecture 12 UMDNJ - School of Health Related Professions EMBL European Molecular Biology Laboratory BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design BankIt (WWW for quick and simple submissions) Lecture 12 Sequin ( Stand -alone sequence submission tool) BINF5011 UMDNJ - School of Health Related Professions Essentials of Bioinformatics/Biotechnology -Drug Design 9 Bioinormatics www.ncbi.nlm.nih.gov GenBank 1 0 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Sequence Databases http://www.embl.org/ European Molecular Biology Laboratory 1 1 Sequence Databases http://www.ebi.ac.uk/ 1 2 European Bioinformatics Institute Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 2 Sequence Databases http://www.ebi.ac.uk/services/index.html 1 3 Sequence Databases http://www.ebi.ac.uk/embl/index.html 4 1 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Sequence Databases http://www.ddbj.nig.ac.jp/ 1 5 Sequence Databases 1 6 DNA Data Bank of Japan http:// www.ebi.ac.uk/embl/Contact/collaboration.html Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Bioinformatics Database 1 7 Protein Data Bank Protein Data Bank Brookhaven Protein Data Bank Research Collaboratory for Structural Bioinformatics Rutgers (The State University of New Jersey) San Diego Supercomputer Center (SDSC) National Institute of Standards and Technology (NIST) http://www.rcsb.edu/pdb/ http://www.pdb.org/ 1 8 Primary Bioinformatics Databases Sequence Database Nucleic Acids (NCBI:GenBank) Proteins Structure Database Proteins (Protein Data Bank) Nucleic Acids (Nucleic Acid Database) Small Molecules (Cambridge Structural Database) Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 3 Protein Data Bank 1 9 Structure Databases:http://ndbserver.rutgers.edu/ 2 0 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Cambridge Structural Database 2 1 http:// www.ccdc.cam.ac.uk Cambridge Structural Database 2 2 http:// www.ccdc.cam.ac.uk Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Structure Databases Cambridge Crystallographic Data Center (CCDC) Established in 1965 in the crystallographic laboratory at the Department of Chemistry, University of Cambridge, UK. To compile a computerized database to record the primary results of crystallographic analyses of small molecules. Cambridge Structural Database was one of the first numerical scientific databases in the world. http://www.ccdc.cam.ac.uk/ Lecture 12 UMDNJ - School of Health Related Professions 2 3 Structural Databases 2 4 BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 4 Structure Databases Cambridge Structural Database (CSD) Records bibliographic, chemical and parimary numerical data from X-ray and neutron diffraction analyses of organics, organometallics, and metal complexes. June 2003 291,965 structures abstracted from around 1000 primary journal sources Lecture 12 UMDNJ - School of Health Related Professions 2 5 Structure Databases June 2003 number of entries number of compounds number of entries with 3D-coordinates number of error-free 3D coordinate sets number of X-ray studies number of neutron studies 291965 264576 261622 255795 290810 1155 2 6 BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Structure Databases Software for Database Access Software for CSD searching, information retrieval, structure visualization, and numerical analysis. ConQuest Start-Programs-CCDC-ConQuest1.6 2 7 Structural Databases 2 8 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Structure Databases 2 9 Structure Databases 3 0 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 5 Secondary (Curated) Sequence Databases - Add value to sequences in primary databases 3 1 Sequence Databases Protein Information Resource A Division of National Biomedical Research Foundation 3 2 http://pir.georgetown.edu/ GenBank SWISS-PROT PIR DDBJ EMBL Direct submissions; Journal scanning Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Sequence Databases 3 3 Sequence Databases SWISS-PROT http://www.ebi.ac.uk/swissprot/index.html 3 4 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Sequence Databases 3 5 Protein Sequence Databases The Uni-Prot/Swiss-Prot Protein Knowledgebase is an annotated protein sequence database established in 1986. The Uni-Prot/Swiss-Prot Protein Knowledgebase is a curated protein sequence database that provides a high level of annotation, a minimal level of redundancy and high level of integration with other databases. 3 6 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 6 Protein Sequence Databases TrEMBL http://www.ebi.ac.uk/trembl/index.html 3 7 Protein Sequence Databases 3 8 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Protein Sequence Databases TrEMBL A protein sequence database of nucleotide translated sequences. The UniProt/TrEMBL sequence database contains the translations of all coding sequences (CDS) present in the DDBJ/EMBL/GenBank Nucleotide Sequence Database and also protein sequences extracted from the literature or submitted to UniProt/Swiss-Prot, which are not yet integrated into UniProt/Swiss-Prot. 3 9 Protein Sequence Databases UniProt (Universal Protein Resource) http://www.ebi.ac.uk/uniprot/index.html The world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. 4 0 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Protein Sequence Databases UniProt (Universal Protein Resource) European Bioinformatics Institute 4 1 Structure Databases NCBI MMDB http://www.ncbi.nlm.nih.gov/Structure/MMDB /mmdb.shtml 4 2 Swiss Institute of Bioinformatics Lecture 12 UMDNJ - School of Health Related Professions Georgetown University BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 7 Structure Databases 4 3 Structure Databases NCBI's structure database is called MMDB (Molecular Modeling DataBase), and it is a subset of three-dimensional structures obtained from the Brookhaven Protein DataBank (PDB), excluding theoretical models. 4 4 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Structure Databases MMDB is a database of ASN.1-formatted records. It was designed for flexibility, and as such, is capable of archiving conventional structural data as well as future descriptions of biomolecules , such as those generated by electron microscopy (surface models 4 5 Structure Databases Abstract Syntax Notation http://asn1.elibel.tm.fr/ 4 6 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Structure Databases 4 7 Structure Databases Macromolecular Structure Database (MSD) EMBL/EBI http://www.ebi.ac.uk/msd/index.html 4 8 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 8 Structure Databases EBI Macromolecular Structure Database 4 9 Structure Databases EBI Macromolecular Structure Database The EBI Macromolecular Structure Database (EMSD) is the European Project for the management and distribution of data on macromolecular structures. Based on the Wellcome Trust Genome campus, next to the beautiful village of Hinxton, approximately ten miles south of Cambridge, UK. 5 0 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Structure Databases EBI Macromolecular Structure Database Goal is to improve the consistency and quality of the world archive of data on macromolecular structures by integrating current database and informatics technologies with a solid core of expertise in structural biology. We collaborate closely with the Research Collaboratory for Structural Bioinformatics (RCSB) who maintain the Protein Data Bank (PDB) in the USA. Structures deposited through the AutoDep tool are processed at the EBI and are then passed to the RCSB. However we are also at the centre of a large, EU-funded project which integrates many aspects different of X -ray crystallography, NMR spectroscopy, electron diffraction and bioinformatics. 5 1 Structure Databases 5 2 Worldwide Protein Data Bank (wwPDB) The Macromolecular Structure Database (MSD/ePDB), the Research Collaboratory for Structural Bioinformatics (RCSB) in the United States and the Protein Data Bank Japan (PDBj) announced a collaboration to form the Worldwide Protein Data Bank (wwPDB)... Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Structure Databases http://www.wwpdb.org / 5 3 Structure Databases 5 4 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 9 Other Types of Databases Genome Sequence Database (GSDB)???? Maintained by National Center for Genome Resources with U.S. DOE Outgrowth of GenBank Collection of DNA sequences related to genome projects 5 5 Other Genome Sequence Database (GSDB) http://www.ncgr.org/ 5 6 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Other Genome Sequence Database (GSDB) http://www.ncgr.org/ 5 7 Other Types of Databases UK Human Genome Mapping Project Resource Centre Medical Research Council 5 8 Closure of Research and Bioinformatics Divisions of RFCGR (formerly HGMPRC) Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Other Types of Databases (contd.) OMIM (NCBI) Online Mendelian Information in Man 5 9 Other Types of Databases (contd.) Physical Mapping Databases GDB (funding discontinued 7/31/98), Genethon, Whitehead, Stanford University The Genome Database:An international collaboration in support of the Human Genome Project Hosted by The Hospital for Sick Children, Toronto, Ontario CANADA 6 0 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 10 Other Types of Databases (contd.) http://www.gdb.org/gdb/ 6 1 Other Types of Databases (contd.) Bibliographic MedLine (Searched via PubMed or Internet Grateful Med) PubMedCentral PUBCRAWLER 6 2 PubCrawler is an alert service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases. Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Other Types of Databases (contd.) 6 3 Other Types of Databases (contd.) Prosite 6 4 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Other Types of Databases (contd.) BLOCKS (http://blocks.fhcrc.org/) 6 5 Other Types of Databases (contd.) REBASE (http://www.hgmp.mrc.ac.uk/Bioinformatics/Databases/rebase -help.html) 6 6 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 11 Other Types of Databases (contd.) ACEDB ACeDB (which stands for "A C. elegans DataBase") started life as the repository for mapping and genomic data for the nematode C. elegans. 6 7 Other Types of Databases (contd.) WIT WIT is short for "What is There". It is similar to the KEGG database in that it tries to integrate all the knowledge there is about an organism. WIT includes a set of over 2900 diagrams depicting metabolic pathways 6 8 KEGG The primary objective of KEGG is to computerise the current knowledge of molecular interactions; namely, metabolic pathways, regulatory pathways and molecular assemblies. Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Web-based Front Ends - Entrez Maintained by NCBI allows retrieval of molecular biology data and bibliographic citations from the NCBI's integrated databases GenBank, EMBL, and DDBJ, SwissProt, PIR, PRF, PDB, Integrated genomes database, MMDB, and Medline Lecture 12 UMDNJ - School of Health Related Professions 6 9 Bioinformatics Databases 7 0 EMBL GenBank DDBJ BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Bioinformatics Databases http://www.ncbi.nlm.nih.gov/Database/index.html 7 1 Bioinformatics Databases 7 2 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 12 Bioinformatics Databases 7 3 Bioinformatics Databases 7 4 Entrez is the integrated, text -based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others. Click on the graphic below for a more detailed view of Entrez integration. Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Web-based Front Ends - SRS For databases supported by EMBL (European Bioinformatics Institute - EBI) Can access many smaller databases Prosite, BLOCKS, transcription factor databases, species -specific databases, databases for specific pathogens Mirror sites (main site in Heidelberg) Serves Europe, Asia, the Pacific, South America Lecture 12 UMDNJ - School of Health Related Professions 7 5 Searching the Databases Some query systems allow wildcards * = match all characters, e.g., lac* (most) # = match one character (NCBI), $ (NCBI) or ? (others) = match zero or one character, e.g., l?c 7 6 Avoid using common words alone in searches Example; DNA, protein Too many hits BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Bioinformatics Databases Building Biological Databases Chapter 13. Developing Bioinformatics Computer Skills Cynthia Gibas & Per Jambeck OReilly & Associates, Inc April 2001 ISBN:1-56592-664-1 7 7 Bioinformatics Databases Steps involved in developing a database designing data model choosing a database management system implementing your data model developing a use-friendly front-end 7 8 Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformatics/Biotechnology -Drug Design 13 Bioinformatics Databases Chap 13. Building Biological Databases Types of Databases Flat File Database Relational Database Object Oriented Databases 7 9 The GenBank Flatfile http://www.ncbi.nlm.nih.gov/Sitemap/samplere cord.html 8 0 ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt Lecture 12 UMDNJ - School of Health Related Professions BINF5011 Essentials of Bioinformati...

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University of Medicine and Dentistry of New Jersey - BINF - 5011
UNIX UNIX BASICS UNIX is case sensitive lower case letters are not the same as upper case letters. Example -l is different from -L1 UNIX commands are normally in lower case Command arguments could be either lower or upper case.Lecture 6UMD
University of Medicine and Dentistry of New Jersey - BINF - 5011
12UNIX UNIX BASICS UNIX is case sensitive lower case letters are not the same as upper case letters. Example -l is different from -LUNIX UNIX BASICS Space Example man -k -k file : option man : command file : argument Please note it's not
University of Medicine and Dentistry of New Jersey - BINF - 5011
1Bioinformatics What is Bioinformatics?Lecture 7UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology-Drug Design2Bioinformatics Why study Bioinformatics? What role does Bioinformatics play in d
University of Medicine and Dentistry of New Jersey - BINF - 5011
12Bioinformatics What is Bioinformatics?Bioinformatics Why study Bioinformatics? What role does Bioinformatics play in drug discovery and development? What is Drug Discovery and Development?Lecture 7UMDNJ - School of Health Related Profe
University of Medicine and Dentistry of New Jersey - BINF - 5011
1Human Bodyhttp:/www.visi.com/~reut eler/vinci/vitruvian.jpgLecture 8UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology-Drug DesignHuman Body : Are you familiar with Anatomy Histology
University of Medicine and Dentistry of New Jersey - BINF - 5011
12Human BodyHuman Body : Are you familiar with Anatomy Histology Physiology Pathology Biochemistry Cell Biology Developmental Biology Genetics Microbiology Molecular Biology Molecular Genetics PharmacologyBINF5011Essentials of Bio
University of Medicine and Dentistry of New Jersey - BINF - 5011
Human Body: MoleculesStructure of Proteins Amino Acids Peptides (oligopeptide, polypeptide) Proteins1Lecture 8UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology-Drug DesignGeneral Structure of an
University of Medicine and Dentistry of New Jersey - BINF - 5011
12Human Body: MoleculesStructure of Proteins Amino Acids Peptides (oligopeptide, polypeptide) ProteinsGeneral Structure of an Amino AcidLecture 8UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnolo
University of Medicine and Dentistry of New Jersey - BINF - 5011
Structure of Nucleic Acids Some Pictures are taken from1 Saenger, W. (1984) Principles of Nucleic Acid Structure, SpingerVerlag, NY. Calladine, C.R. & Drew, H.R. (1992) Understanding DNA: The molecule and How it Works, Academic Press, NY.Lect
University of Medicine and Dentistry of New Jersey - BINF - 5011
123Structure of Nucleic Acids Some Pictures are taken fromStructure of Nucleic AcidsN7Structure of Nucleic AcidsCH HC4 5 6CH C5 6N3 2N1HC8NH9C4CH N3 2HC NH1CH Saenger, W. (1984) Principles of Nucleic Acid St
University of Medicine and Dentistry of New Jersey - BINF - 5011
UNIX Workstations How to login and what happen then? Depends on what workstation you are using.1Lecture 3UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology-Drug DesignAccess to UMDNJ Computers
University of Medicine and Dentistry of New Jersey - BINF - 5011
12UNIX Workstations How to login and what happen then? Depends on what workstation you are using.Access to UMDNJ Computers Non-X window Environment SSH with non x-window terminal type VNC X-window Environments PC with Linux PC with X-w
University of Medicine and Dentistry of New Jersey - BINF - 5011
UNIX Editor pico More Common Editors vi, emacs Screen Oriented Editor nedit (SGI), jot dtpad HP (njmsa) type:/usr/dt/bin/dtpad file_name1Lecture 4UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology-
University of Medicine and Dentistry of New Jersey - BINF - 5011
12UNIX Editor pico More Common Editors vi, emacs Screen Oriented Editor nedit (SGI), jot dtpad HP (njmsa) type:/usr/dt/bin/dtpad file_nameUNIX Vi Learning the vi Editor Linda Lamb & Arnold Robbins O'Reilly & Associates ISBN 1-56592-426-6
University of Medicine and Dentistry of New Jersey - BINF - 5011
1Bioinformatics What is Bioinformatics?Lecture 5UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology-Drug Design2Bioinformatics What is Bioinformatics? Does a use of Computer make any fields to
University of Medicine and Dentistry of New Jersey - BINF - 5011
12Bioinformatics What is Bioinformatics?Bioinformatics What is Bioinformatics? Does a use of Computer make any fields to be Bioinformatics? Bioinformatics - in 1990s, many different definitions.Lecture 5UMDNJ - School of Health Related P
University of Medicine and Dentistry of New Jersey - LEC - 5011
ACS:\Remote Usage1 SSH - rlogin and telnet are insecure protocols, and upon logging in with one of these protocols, passwords are sent across the network in clear text, that can be read by any industrious individual with the right software. Pleas
University of Medicine and Dentistry of New Jersey - LEC - 5011
ACS:\Remote Usage12Access to UMDNJ Computers: Use of secure protocol is recommended by ACS. telnet => ftp => ssh sftp SSH - rlogin and telnet are insecure protocols , and upon logging in with one of these protocols, passwords are sent acro
University of Medicine and Dentistry of New Jersey - LEC - 5011
SFTP 1) Simple Secure FTP 2) Secure FTP with tunneling1Lecture 2UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology-Drug DesignSFTP 1) Simple Secure FTP2Lecture 2UMDNJ - School of Health Re
University of Medicine and Dentistry of New Jersey - LEC - 5011
12SFTP 1) Simple Secure FTP 2) Secure FTP with tunnelingSFTP 1) Simple Secure FTPLecture 2UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology -Drug DesignLecture 2UMDNJ - School of Health R
University of Medicine and Dentistry of New Jersey - LEC - 5011
CYGWIN Cygwin/Xfree861Lecture 2UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology-Drug DesignCYGWIN?XFree862 Cygwin/XFree86 is a port of XFree86 to the Microsoft Windows family of operating s
University of Medicine and Dentistry of New Jersey - LEC - 5011
12CYGWIN Cygwin/Xfree86CYGWIN?XFree86 Cygwin/XFree86 is a port of XFree86 to the Microsoft Windows family of operating systems.Lecture 2UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology -Drug
University of Medicine and Dentistry of New Jersey - LEC - 5011
VNC Alternatively, you can use VNC, Virtual Network Computing.1Lecture 2UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology-Drug DesignVNC: http:/www.realvnc.com/2Lecture 2UMDNJ - School of H
University of Medicine and Dentistry of New Jersey - LEC - 5011
12VNC Alternatively, you can use VNC, Virtual Network Computing.VNC: http:/www.realvnc.com/Lecture 2UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology -Drug DesignLecture 2UMDNJ - School of
University of Medicine and Dentistry of New Jersey - LEC - 5011
12General InformationBINF5011:Essentials of Bioinformatics/Biotechnology-Drug DesignStarts at 6:00 pm todayLecture 1UMDNJ - School of Health Related ProfessionsBINF5011Essentials of Bioinformatics/Biotechnology -Drug DesignLecture 1UMD
University of Medicine and Dentistry of New Jersey - LEC - 5011
Introduction to the World-Wide Web Large scale on-line repository of information Can be accessed and searched using a browser Hypertext, hypermedia, and HTML Text stored in electronic form with cross-reference links between pages is called hypert
University of Medicine and Dentistry of New Jersey - LEC - 5011
12Introduction to the World-Wide Web Large scale on-line repository of information Can be accessed and searched using a browser Hypertext, hypermedia, and HTML Text stored in electronic form with cross-reference links between pages is called
University of Medicine and Dentistry of New Jersey - BINF - 5210
vti_encoding:SR|utf8-nl vti_timelastmodified:TR|17 Feb 2004 15:16:42 -0000 vti_extenderversion:SR|4.0.2.7802 vti_cacheddtm:TX|17 Feb 2004 15:16:42 -0000 vti_filesize:IR|40960 vti_cachedlinkinfo:VX|H|http:/home.ubalt.edu/ntsbarsh/index.html H| http:/w
University of Medicine and Dentistry of New Jersey - BINF - 5210
vti_encoding:SR|utf8-nl vti_timelastmodified:TR|25 Mar 2003 19:17:32 -0000 vti_extenderversion:SR|4.0.2.7802 vti_cacheddtm:TX|25 Mar 2003 19:17:32 -0000 vti_filesize:IR|61440 vti_cachedlinkinfo:VX|H|http:/bmj.com/cgi/ijlink? linkType=ABST&journalCode
University of Medicine and Dentistry of New Jersey - BINF - 5210
vti_encoding:SR|utf8-nl vti_timelastmodified:TR|17 Feb 2004 21:26:28 -0000 vti_extenderversion:SR|4.0.2.7802 vti_cacheddtm:TX|17 Feb 2004 21:26:28 -0000 vti_filesize:IR|613888 vti_cachedlinkinfo:VX|H|http:/www.stat.ucla.edu/%7Ecochran/stat10/winter/l
University of Medicine and Dentistry of New Jersey - BINF - 5210
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