Transcript - Cal State LA - Instructional Web Server

An Introduction to
NCBI & BLAST
National Center for
Biotechnology Information
Richard Johnston
Pasadena City College
Background and Origin

Congress established the National Center for Biotechnology
Information (NCBI) on November 4, 1988
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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.
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Website
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http://www.ncbi.nlm.nih.gov/
http://www.ncbi.nlm.nih.gov/About/glance/ourmission.html
NCBI Activities
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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
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…(more)
NCBI Activities2
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Supports training on basic and applied research in
computational biology for postdoctoral fellows through the
NIH Intramural Research Program
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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
NCBI Resources
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
http://www.ncbi.nlm.nih.gov/About/index.html
Databases

ENTREZ DATABASES
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LITERATURE DATABASES
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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

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Together, NCBI's literature databases constitute an extended searchable library
of the life sciences literature.
NUCLEOTIDE DATABASES

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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.
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
Tools
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Literature search

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Tools for Sequence Analysis
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PubMed provides tools to access the available literature,
including full-text articles and online books.
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
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.
BLAST Uses
Using BLAST, researchers can gain
understanding about genes and sequences by
comparing them to known sequences in NCBI’s
database.
Courses and Tutorials Offered by NCBI:
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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
Tutorials
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Digital World Biology tutorials and worksheets
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NCBI Pub Med Tutorial
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http://www.digitalworldbiology.com/dwb/Tutorials/
http://www.digitalworldbiology.com/BLAST/62000sequences.html
http://www.digitalworldbiology.com/activities/BLASTing_through_the_
kingdom_of_life_2009.pdf
http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/
NCBI BLAST Tutorials
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http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html
http://www.ncbi.nlm.nih.gov/Education/index.html