Database Resources of the National
Center for Biotechnology
Information
David L. Wheeler et al. Nucleic Acids Research, Vol. 33,
Database issue
Baharak Rastegari
MEDG 505 presentation
February 3, 2005
baharak@cs.ubc.ca
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NCBI! What is it?
• Created in 1998
• At the National Institutes of Health
• To develop information systems for molecular
biology
• Maintains: GenBank(R) nucleic acid sequence
database
• Provides: Data retrieval systems & computational
resources
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DB Resources Categories
• Databases retrieval tools
• The BLAST family of sequence-similarity
search programs
• Resources for Gene-level sequences
• Resources for Genome-scale analysis
• Resources for the analysis of patterns of
gene expression and phenotypes
• The molecular modeling database, the
conserved domain database search, CDART
and Protein interactions
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DB Resources Categories
• Databases retrieval tools
• The BLAST family of sequence-similarity
search programs
• Resources for Gene-level sequences
• Resources for Genome-scale analysis
• Resources for the analysis of patterns of
gene expression and phenotypes
• The molecular modeling database, the
conserved domain database search, CDART
and Protein interactions
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Entrez
• Text searching
→ using Boolean queries
→ of a diverse set of over 20 databases
• Simultaneous searches across all Entrez
databases at speeds comparable to a single
database search
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Entrez
• Retrieved record can be displayed in a wide
variety of formats
→ GenBank Flatfile, FASTA, XML, …
• Graphical display is offered for some type of
records
• Search history
→ allows users to recall result of previous searches
and combine them using Boolean logic
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Entrez
• PubMed
→ includes 12.8 million references and abstracts in
MEDLINE(R)
→ with links to the full text of more than 4400
journals available on web
• PubMed Central
→ digital archive of peer reviewed journals in life
sciences
→ access to over 300 000 full text articles
→ over 160 journals
• Books database
→ Contains more than 35 online scientific textbook
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Taxonomy
• Indexed over 165 000 named organisms
• Can be used to view taxonomic position or retrieve
data from a database for particular organism or
group
• Searches can be made on whole, partial or
phonetically spelled organism names
• Links to organisms commonly used in biological
research are provided
• Display custom taxonomic trees, representing userdefined subsets of the full NCBI taxonomy
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Entrez Gene
• Successor to LocusLink
• Provides an interface to curated sequences
and descriptive information about genes
• With links to gene related resources
→ NCBI’s Map Viewer, Evidence Viewer, Blast Link, ..
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DB Resources Categories
• Databases retrieval tools
• The BLAST family of sequence-similarity
search programs
• Resources for Gene-level sequences
• Resources for Genome-scale analysis
• Resources for the analysis of patterns of
gene expression and phenotypes
• The molecular modeling database, the
conserved domain database search, CDART
and Protein interactions
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BLAST Family
• BLAST
→ Local alignment search tool
→ performing sequence-similarity searches against
variety of sequence databases
→ returning a set of gapped alignments btw the
query and database sequences
• BLAST2Sequences
→ comparing two DNA or protein sequences
→ producing a dot-plot representation of the
alignments
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BLAST Family
• MegaBLAST
→ designed to search for nearly exact matches
→ handles batch nucleotide queries
→ operates up to 10 times faster than standard
nucleotide BLAST
• BLASTLink (BLink)
→ displays pre-computed protein BLAST alignments
for each protein in the Entrez databases
→ can display subset of these alignments by
taxonomic criteria, database of origin, …
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DB Resources Categories
• Databases retrieval tools
• The BLAST family of sequence-similarity
search programs
• Resources for Gene-level sequences
• Resources for Genome-scale analysis
• Resources for the analysis of patterns of
gene expression and phenotypes
• The molecular modeling database, the
conserved domain database search, CDART
and Protein interactions
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UniGene
• System for automatically partitioning Gen-Bank
sequences, including ESTs, into a non-redundant set of
gene-oriented clusters
• Each cluster contains sequences that represent a
unique gene, and is linked to related information
• Human UniGene
→ over 4.5 million human ESTs
→ reduced to 42-fold in number to approximately 107 000
sequence clusters
• Has been used as a source of unique sequences for the
fabrication of microarrays for the large-scale study
of gene expression
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ProEST
• Analogous to BLASTLink
• Presents pre-computed BLAST alignment btw
protein sequences from model organisms and
six-frame translations of UniGene nucleotide
sequences
• Reports are updated in tandem with UniGene
protein similarities
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Trace & Assembly Archives
• Trace Archive allows for flexible searching
and download of sequencing traces
• Assembly Archive links the raw sequence
information found in the Trace Archive with
assembly information found in GenBank
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HomoloGene
• System for automated detection of homologs
among the annotated genes of several
completely sequence eukaryotic
• New HomoloGene build is guided by the
taxonomic tree, relies on:
→ conserved gene order & measures of DNA similarity
among closely related species
→ protein similarity for more distantly related
organisms
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…HomoloGene
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‘Ancestor’ field
→ refers to the taxonomic group of the last common ancestor of
the species represented in HomoloGene entry
→ using it is possible to limit a search to genes conserved in one
of 22 ancestral group
• ‘Pairwise Score’ display gives a table of pairwise
statistics for members of a Homologene group that
includes
→ percent amino acid and nucleotide identities
→ Jukes-Cantor genetic distance parameter
→ the ratio of non-synonymous to synonymous amino acid
substitutions (Ka/Ks)
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Reference Sequences
• RefSeq provides curated references for
→ transcripts, proteins and genomic regions
→ computationally derived nucleotide sequences and
proteins
• Containing 1.3 million sequences
→ including more than 1 million protein sequences
→ representing more than 2400 organisms
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ORF Finder and Spidey
• ORF finder
→ performs a six-frame translation of a nucleotide
sequence
→ returns the location of each ORF within a specified
size range
• Spidey
→ alignment tool for eukaryotic genomic sequences
→ takes into account predicted splice sites in
constructing its alignment, and can use one of four
splice-site models
→ returns exon alignments, protein translations and a
summary showing the alignment quality, …
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Electronic PCR (e-PCR)
• Forward e-PCR
→ searches for matches to STS primer pairs in the
UniSTS database of over 450 000 markers
→ to increase sensitivity, allows the size of primer
segment to be matched, number of mismatches,
number of gaps and the size of the STS to be
adjusted
• Reverse e-PCR
→ used to estimate the genomic binding site, amplicon
size and specificity for sets of primer pairs by
searching against the genomic and transcript
databases
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dbSNP
• Database of single nucleotide polymorphisms
• Repository for single base nucleotide
substitutions and short deletion and insertion
polymorphisms
• Contains 9.8 million human SNPs as well as about
5 million from a variety of other organisms
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DB Resources Categories
• Databases retrieval tools
• The BLAST family of sequence-similarity
search programs
• Resources for Gene-level sequences
• Resources for Genome-scale analysis
• Resources for the analysis of patterns of
gene expression and phenotypes
• The molecular modeling database, the
conserved domain database search, CDART
and Protein interactions
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Entrez Genomes
• Provides access to genomic data contributed by the
scientific community for species whose sequencing and
mapping is complete or in progress
• Includes:
→ over 180 complete microbial genomes
→ more than 1600 viral genomes
→ over 550 reference sequences for eukaryotic organelles
→…
• Complete genome can be accessed hierarchically starting
from either
→ an alphabetical listing
→ phylogenetic tree for each of six principal taxonomic groups
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COGs database
• Clusters of orthologous groups
• Presents a compilation of orthologous groups of
proteins from 66 completely sequenced
organisms
• Eukaryotic version, KOGs, is available for seven
eukaryotes
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MAP & Evidence Viewer
• MAP Viewer displays
→ genome assemblies
→ genetic and physical markers
→ the result of annotation, and other analyses using
sets of aligned maps
• Evidence Viewer displays the alignments to a
→ genomic contig of RefSeq transcripts
→ GenBank mRNAs
→ known or potential transcripts
→ EST’s supporting a gene model
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Cancer Chromosome
• Consists of
→ NCI/NCBI SKY, M-FISH and CGH databases
→ NCI Mitelman database of chromosome Aberrations
in cancer
→ NCI Recurrent Chromosome Aberrations in Cancer
dtabase
• Three search formats are available
→ convential Entrez query
→ Quick/Simple search: set of menus to select a
disease site or diagnosis
→ Advanced search : combination of forms for more
complex queries
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DB Resources Categories
• Databases retrieval tools
• The BLAST family of sequence-similarity
search programs
• Resources for Gene-level sequences
• Resources for Genome-scale analysis
• Resources for the analysis of patterns of
gene expression and phenotypes
• The molecular modeling database, the
conserved domain database search, CDART
and Protein interactions
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SAGEmap
• Provides two-way mapping btw
→ regular (10 base) and LongSAGE (17 base) SAGE tags
→ UniGene clusters
• SAGEmap repository contains
→ 381 SAGE experiments from 11 organisms
• Can also construct a user-configurable table of
data comparing one group of SAGE libraries with
another
• Is updated weekly
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Gene Expression Ominbus
• Data repository and retrieval system for any highthroughput gene expression or molecular abundance data
• Contains
→ microarray-based experiments measuring the abundance of
mRNA
→ genomic DNA and protein molecules
→ non-array-based technologies such as SAGE
→ mass spectrometry peptide profiling
• Now contains
→ high-throughput gene expression data from about 30 000
hybridization experiment
→ about 1000 array definitions
→ half a billion individual spot measurement data derived from
over 100 organisms
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OMIM
• Catalog of human genes and genetic disorders
authored and edited by Victor A. McKusick at
the John Hopkins University
• Contains information on disease phenotypes and
genes
• Contains
→ about 16 000 entries
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DB Resources Categories
• Databases retrieval tools
• The BLAST family of sequence-similarity
search programs
• Resources for Gene-level sequences
• Resources for Genome-scale analysis
• Resources for the analysis of patterns of
gene expression and phenotypes
• The molecular modeling database, the
conserved domain database search, CDART
and Protein interactions
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MMDB
• Built by processing entries from the Protein
Data Bank
• Structures are linked to sequences in Entrez and
to the Conserved Domain Database.
• Conserved Domain Search can be used to search
a protein sequence for conserved domains in
CDD
• Wherever possible, CDD hits are linked to
structure which can be viewed with NCBI’s 3D
molecular structure viwer, Cn3D
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HIV-I/Human Protein Interaction DB
• Concise summary of documented interactions
between HIV-1 proteins and
→ host cell proteins
→ other HIV-1 proteins
→ proteins from disease organisms associated with HIV
or AIDS
• Summaries, including protein RefSeq accession
numbers, Entrez Gene ID number, … are
presented
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Summary / Conclusion
• NCBI provides many tools for data retrieval and
analysis of data in GenBank and other biological
data
• All of the tools and resources can be find easily
on the website http://www.ncbi.nih.gov/ along
with documentations and explanatory material
• NCBI Handbook and several tutorials are
available
• One can search for tools and information in
NCBI website by choosing NCBI Website as
database
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Thank you!
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Outline
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Introduction
Related work
Components of a Pseudoknotted Sec. Str.
Parsing algorithm
Enumerating loops
Akutsu’s structure class
Conclusion & Future work
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