NCBI: something old, something new. What is NCBI? Create automated systems for knowledge about molecular biology, biochemistry, and genetics. Perform.

Slides:

Advertisements

Similar presentations

Databases (“knowledge bases”) used in genome analysis

Advertisements

Creating NCBI The late Senator Claude Pepper recognized the importance of computerized information processing methods for the conduct of biomedical research.

Genome databases and webtools for genome analysis Become familiar with microbial genome databases Use some of the tools useful for analyzing genome Visit.

NCBI web resources I: databases and Entrez Yanbin Yin Fall 2014 Most materials are downloaded from ftp://ftp.ncbi.nih.gov/pub/education/ 1.

The National Center for Biotechnology Information (NCBI) a primary resource for molecular biology information Database Resources.

Pharmacy Information Resources TTUHSC Preston Smith Library presents Rev. 08/2014.

The design, construction and use of software tools to generate, store, annotate, access and analyse data and information relating to Molecular Biology.

NATIONAL LIBRARY OF MEDICINE The PubMed ID and Entrez, PubMed and PubMed Central Edwin Sequeira National Center for Biotechnology Information June 21,

How to use the web for bioinformatics Molecular Technologies Ethan Strauss X 1171

Bioinformatics and the Engineering Library ASEE 2008 Amy Stout.

Archives and Information Retrieval

Sequence Analysis MUPGRET June workshops. Today What can you do with the sequence? What can you do with the ESTs? The case of SNP and Indel.

Bioinformatics and Phylogenetic Analysis

Lecture 2.21 Retrieving Information: Using Entrez.

Kate Milova MolGen retreat March 24, Microarray experiments: Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.

Biological Databases Notes adapted from lecture notes of Dr. Larry Hunter at the University of Colorado.

Molecular Evidence Using DNA, RNA or Protein Sequences to Classify Organisms.

Biological Databases Chi-Cheng Lin, Ph.D. Associate Professor Department of Computer Science Winona State University – Rochester Center

Kate Milova MolGen retreat March 24, Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.

Genomic Database - Ensembl Ka-Lok Ng Department of Bioinformatics Asia University.

The Protein Data Bank (PDB)

Kate Milova MolGen retreat March 24, Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.

Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

We are developing a web database for plant comparative genomics, named Phytome, that, when complete, will integrate organismal phylogenies, genetic maps.

Sequence Analysis. Today How to retrieve a DNA sequence? How to search for other related DNA sequences? How to search for its protein sequence? How to.

How to use the web for bioinformatics Ethan Strauss X 1171

Kate Milova MolGen retreat March 24, Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.

Doug Brutlag Professor Emeritus Biochemistry & Medicine (by courtesy) Genome Databases Computational Molecular Biology Biochem 218 – BioMedical Informatics.

Introductory Overview

Bioinformatics.

Development of Bioinformatics and its application on Biotechnology

Searching PubMed® NCBI, NLM Resources, Micromedex -GSBS TTUHSC Preston Smith Library presents Rev. 08/17/14.

1 Database Resources of the National Center for Biotechnology Information Baharak Rastegari MEDG 505 presentation February 3, 2005 David.

NCBI FieldGuide NCBI Molecular Biology Resources January 2008 Using Entrez.

Doug Raiford Lesson 3.  More and more sequence data is being generated every day  Useless if not made available to other researchers.

BIOINFORMATICS IN BIOCHEMISTRY Bioinformatics– a field at the interface of molecular biology, computer science, and mathematics Bioinformatics focuses.

BioHealthBase: A Web-based Database and Analysis Resource for Francisella Shubhada Godbole 1, Jyothi Noronha 1, Burke Squires 1, Victoria Hunt 1, Ed Klem.

NCBI Vector-Parasite Genomic Related Databases Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 12, 2004

Part I: Identifying sequences with … Speaker : S. Gaj Date

Genome databases and webtools for genome analysis Become familiar with microbial genome databases Use some of the tools useful for analyzing genome Visit.

جلسه اول بیو انفورماتیک گردآوری:مسعود رسول آبادی

-- Don Preuss NCBI/NLM/NIH

Organizing information in the post-genomic era The rise of bioinformatics.

Gramene Objectives Provide researchers working on grasses and plants in general with a bird’s eye view of the grass genomes and their organization. Work.

NCBI FieldGuide NCBI Molecular Biology Resources March 2007 Using Entrez.

NCBI Literature Databases: PubMed

EB3233 Bioinformatics Introduction to Bioinformatics.

Algorithms for Biological Sequence Analysis Kun-Mao Chao ( 趙坤茂 ) Department of Computer Science and Information Engineering National Taiwan University,

Bioinformatics and Computational Biology

Computer Storage of Sequences

An Introduction to NCBI & BLAST National Center for Biotechnology Information Richard Johnston Pasadena City College.

Information retrieval and sliding window programs April 5, 2011 Hand in Homework #1. Homework #2 due Tuesday, April 12. Learning objectives- Understand.

Welcome to the Protein Database Tutorial. This tutorial will describe how to navigate the section of Gramene that provides collective information on proteins.

The Bovine Genome Database Abstract The Bovine Genome Database (BGD, facilitates the integration of bovine genomic data. BGD is.

 What is MSA (Multiple Sequence Alignment)? What is it good for? How do I use it?  Software and algorithms The programs How they work? Which to use?

NCBI PubMed NCBI Literature Databases: PubMed Session #1, April 28, 2005 Session #2, April 29, 2005 Ho Chi Minh City, VietNam.

Entrez, dbSNP, GEO, OMIM & LinkOut JanPlan Entrez Distributed by NCBI in 1991 on CD-ROM Included linked nodes: GenBank & PDB Translated GenBank,

Introduction to PubChem BioAssay

Biological Databases By: Komal Arora.

NCBI Molecular Biology Resources

Archives and Information Retrieval

Bioinformatics Madina Bazarova. What is Bioinformatics? Bioinformatics is marriage between biology and computer. It is the use of computers for the acquisition,

What is Bioinformatics?

Functional Annotation of the Horse Genome

Genome Annotation Continued

Explore Evolution: Instrument for Analysis

Lesson 3 Bioinformatics Laboratory

Dissemination of the mcr-1 colistin resistance gene

Problems from last section

SUBMITTED BY: DEEPTI SHARMA BIOLOGICAL DATABASE AND SEQUENCE ANALYSIS.

Presentation transcript:

NCBI: something old, something new

What is NCBI? Create automated systems for knowledge about molecular biology, biochemistry, and genetics. Perform research into advanced methods of analyzing and interpreting molecular biology data. Enable biotechnology researchers and medical care personnel to use the systems and methods developed. On November 4, 1988 that President Ronald Reagan signed the Health Omnibus Extension Act to create The National Center for Biotechnology Information as part of National Library of Medicine at NIH.

The National Center for Biotechnology Information (NCBI) Part of National Library of Medicine (NLM) at National Institutes of Health (NIH) Bethesda,MD

NCBI: down on the farm Genome assembly and annotation Pre-computed relationships for: –Protein clusters –“Nearby” nucleic acid –EST unigene clusters –Putative homologous genes –Conserved protein domains –SNPs –Reciprocal links

Web users: 2.7 million per day Data downloaded: 23 TB per day Peak web hits: 7,000 per second Web page views: 26 million per day NCBI Daily Users

NCBI: Integrated platform for data analysis and visualization Primary Data sets: BioProject, BioSample, Genome, Assembly, Annotation Curated data sets: Refseq genomes, Gene, Protein Clusters, Pathogenic Factors, Targeted Loci Entrez search and retrieval system Analysis Tools: Annotation pipeline, genome alignments, protein clustering, multiple alignments, (assembly, SNP) Validation Tools: assembly and annotation quality assesment Visualization Tools: genomeMap, distance tree, proteinMap, Genome Comparison

How to navigate through NCBI resources Text search in Entrez Search in MapViewer All databases Marker/gene name Specialized databases Accession # Use limits page Organism name Sequence search Pre-computed similarities BLAST Blink Genome BLAST CDD Splign/ProSplign TaxPlot Use Genome specific resources

Getting Started: NCBI Home Page Search All Databases in Entrez Learn more: Newsletter Education mailing lists Search resources by name

NCBI Resources by name

How to: NCBI help pages

The NCBI Handbook

Keeping up with what’s new NCBI News on Bookshelf NCBI News on Bookshelf

Genetic Testing Registry (GTR)

BLAST

Entrez Assembly

Entrez Genome redesign

Microbial Genome Resources

NCBI on Facebook and Twitter

David Lipman on GenBank 25 th Anniversary