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

2. Background and Origin  Congress established the National Center for Biotechnology Information (NCBI) on November 4, 1988  NCBI's mission is to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease.  Website  http://www.ncbi.nlm.nih.gov/ http://www.ncbi.nlm.nih.gov/  http://www.ncbi.nlm.nih.gov/About/glance/ourmission.html http://www.ncbi.nlm.nih.gov/About/glance/ourmission.html

3. NCBI Activities  Conducts research on fundamental biomedical problems at the molecular level using mathematical and computational methods  Maintains collaborations with several NIH institutes, academia, industry, and other governmental agencies  Fosters scientific communication by sponsoring meetings, workshops, and lecture series  …(more)

4. NCBI Activities 2  Supports training on basic and applied research in computational biology for postdoctoral fellows through the NIH Intramural Research Program  Engages members of the international scientific community in informatics research and training through the Scientific Visitors Program  Develops, distributes, supports, and coordinates access to a variety of databases and software for the scientific and medical communities  Develops and promotes standards for databases, data deposition and exchange, and biological nomenclature

6. NCBI Resources http://www.ncbi.nlm.nih.gov/About/index.html NCBI has a bewildering array of resources. We will provide an overview of what NCBI has to offer, but only some resources will be used in this class. Browse the links on this page to get an idea of range of information and tools available

7. Databases  ENTREZ DATABASES  Entrez integrates the scientific literature, DNA and protein sequence databases, 3D protein structure and protein domain data, and other information into a tightly interlinked system.  LITERATURE DATABASES  Together, NCBI's literature databases constitute an extended searchable library of the life sciences literature.  NUCLEOTIDE DATABASES  NCBI's sequence databases accept genome data from sequencing projects from around the world and serve as the cornerstone of bioinformatics research.  GENOME-SPECIFIC RESOURCES  NCBI provides access to the whole genomes of over 1,000 organisms. Genomes represent both completely sequenced organisms and those for which sequencing is in progress.  …plus many others

8. Tools  Literature search  PubMed provides tools to access the available literature, including full-text articles and online books.  Tools for Sequence Analysis  Tools such as BLAST provide the ability to search for, compare, and analyze gene and protein sequences  Tools for 3-dimensional structure analysis  The program Cn3D allows protein structures to be displayed and manipulated

9. BLAST Basic Local Alignment Search Tool The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between protein or nucleotide sequences. The program compares nucleotide or protein sequences to sequence in a database and calculates the statistical significance of the matches.

10. BLAST Uses Using BLAST, researchers can gain understanding about genes and sequences by comparing them to known sequences in NCBI’s database.

11. Courses and Tutorials Offered by NCBI :  Getting Started  A Field Guide to GenBank and NCBI Molecular Biology Resources  Medical Library Assoc. Course on Molecular Biology Information  Blast Information Guide  Entrez Tutorials  Structure Tutorial  Pub Med Online Tutorial  PubMed Tour  Genes and Disease  Coffee Break http://www.ncbi.nlm.nih.gov/Education/index.html http://www.ncbi.nlm.nih.gov/About/outreach/courses.html

12. Tutorials  Digital World Biology tutorials and worksheets  http://www.digitalworldbiology.com/dwb/Tutorials/ http://www.digitalworldbiology.com/dwb/Tutorials/  http://www.digitalworldbiology.com/BLAST/62000sequences.html http://www.digitalworldbiology.com/BLAST/62000sequences.html  http://www.digitalworldbiology.com/activities/BLASTing_through_the_ kingdom_of_life_2009.pdf http://www.digitalworldbiology.com/activities/BLASTing_through_the_ kingdom_of_life_2009.pdf  NCBI Pub Med Tutorial  http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/ http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/  NCBI BLAST Tutorials  http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html  http://www.ncbi.nlm.nih.gov/Education/index.html http://www.ncbi.nlm.nih.gov/Education/index.html