Transcript No Slide Title

Introduction to Bioinformatics Databases
Central dogma of molecular biology
DNA
RNA
protein
phenotype
A main focus of bioinformatics is to study molecular sequence
data to gain insight into a broad range of biological problems.
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After Pace NR (1997)
Science 276:734
With the use of bioinformatics we can learn the variation that
occur between species, and we can deduce the evolutionary
history of life on Earth.
70
60
50
40
30
20
10
0
Base pairs of
DNA (billions)
Sequences (millions)
Growth of GenBank
1985
December
1982
1990
1995
2000
June
2006
Base pairs of
DNA (billions)
Growth of the International Nucleotide
Sequence Database Collaboration
Base pairs contributed by GenBank
EMBL
DDBJ
http://www.ncbi.nlm.nih.gov/Genbank/
Central dogma of molecular biology
DNA
genome
RNA
transcriptome
protein
proteome
Central dogma of bioinformatics and genomics
DNA
genomic
DNA
databases
RNA
cDNA
ESTs
UniGene
protein
phenotype
protein
sequence
databases
Fig. 2.2
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There are three major public DNA databases
EMBL
GenBank
DDBJ
The underlying raw DNA sequences are identical
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There are three major public DNA databases
EMBL
Housed
at EBI
European
Bioinformatics
Institute
GenBank
DDBJ
Housed
at NCBI
National
Center for
Biotechnology
Information
Housed
in Japan
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>300,000 species are represented in GenBank
Table 2-1
Taxonomy nodes at NCBI
8/06
http://www.ncbi.nlm.nih.gov/Taxonomy/txstat.cgi
The most sequenced organisms in GenBank
Homo sapiens
Mus musculus
Rattus norvegicus
Danio rerio
Zea mays
Oryza sativa
Drosophila melanogaster
Gallus gallus
Arabidopsis thaliana
Updated 8-12-04
GenBank release 142.0
10.7 billion bases
6.5b
5.6b
1.7b
1.4b
0.8b
0.7b
0.5b
0.5b
Table 2-2
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The most sequenced organisms in GenBank
Homo sapiens
Mus musculus
Rattus norvegicus
Danio rerio
Bos taurus
Zea mays
Oryza sativa (japonica)
Xenopus tropicalis
Canis familiaris
Drosophila melanogaster
Updated 8-29-05
GenBank release 149.0
11.2 billion bases
7.5b
5.7b
2.1b
1.9b
1.4b
1.2b
0.9b
0.8b
0.7b
Table 2-2
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The most sequenced organisms in GenBank
Homo sapiens
Mus musculus
Rattus norvegicus
Bos taurus
Danio rerio
Zea mays
Oryza sativa (japonica)
Strongylocentrotus purpurata
Sus scrofa
Xenopus tropicalis
Updated 7-19-06
GenBank release 154.0
12.3 billion bases
8.0b
5.7b
3.5b
2.5b
1.8b
1.5b
1.2b
1.0b
1.0b
Table 2-2
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National Center for Biotechnology
Information (NCBI)
www.ncbi.nlm.nih.gov
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Types of Data in GenBank
 DNA level
 RNA level (cDNA)
 Protein sequences.
…
www.ncbi.nlm.nih.gov
Fig. 2.5
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Fig. 2.5
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PubMed is…
• National Library of Medicine's search service
• 16 million citations in MEDLINE
• links to participating online journals
• PubMed tutorial (via “Education” on side bar)
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Entrez integrates…
• the scientific literature;
• DNA and protein sequence databases;
• 3D protein structure data;
• population study data sets;
• assemblies of complete genomes
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Entrez is a search and retrieval system
that integrates NCBI databases
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BLAST is…
• Basic Local Alignment Search Tool
• NCBI's sequence similarity search tool
• supports analysis of DNA and protein databases
• 100,000 searches per day
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OMIM is…
•Online Mendelian Inheritance in Man
•catalog of human genes and genetic disorders
•edited by Dr. Victor McKusick, others at JHU
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Books is…
• searchable resource of on-line books
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TaxBrowser is…
• browser for the major divisions of living organisms
(archaea, bacteria, eukaryota, viruses)
• taxonomy information such as genetic codes
• molecular data on extinct organisms
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Structure site includes…
• Molecular Modelling Database (MMDB)
• biopolymer structures obtained from
the Protein Data Bank (PDB)
• Cn3D (a 3D-structure viewer)
• vector alignment search tool (VAST)
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Accessing information on
molecular sequences
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Accession numbers are labels
for sequences
NCBI includes databases (such as GenBank) that contain
information on DNA, RNA, or protein sequences.
You may want to acquire information beginning with a
query such as the name of a protein of interest, or the
raw nucleotides comprising a DNA sequence of interest.
DNA sequences and other molecular data are tagged with
accession numbers that are used to identify a sequence
or other record relevant to molecular data.
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What is an accession number?
An accession number is label that used to identify a
sequence. It is a string of letters and/or numbers that
corresponds to a molecular sequence.
Examples (all for retinol-binding protein, RBP4):
X02775
NT_030059
Rs7079946
GenBank genomic DNA sequence
Genomic contig
dbSNP (single nucleotide polymorphism)
DNA
N91759.1
NM_006744
An expressed sequence tag (1 of 170)
RefSeq DNA sequence (from a transcript)
RNA
NP_007635
AAC02945
Q28369
1KT7
RefSeq protein
GenBank protein
SwissProt protein
Protein Data Bank structure record
protein
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Four ways to access DNA and
protein sequences
[1] Entrez Gene with RefSeq
[2] UniGene
[3] European Bioinformatics Institute (EBI)
and Ensembl (separate from NCBI)
[4] ExPASy Sequence Retrieval System
(separate from NCBI)
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4 ways to access protein and DNA sequences
[1] Entrez Gene with RefSeq
Entrez Gene is a great starting point: it collects
key information on each gene/protein from
major databases. It covers all major organisms.
RefSeq provides a curated, optimal accession
number for each DNA (NM_006744)
or protein (NP_007635)
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From the NCBI home
page, type “rbp4”
and hit “Go”
revised
Fig. 2.7
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revised
Fig. 2.7
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By applying limits, there are now just two entries
Entrez Gene (top of page)
Note that links to
many other RBP4
database entries
are available
revised
Fig. 2.8
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Entrez Gene (middle of page)
Entrez Gene (bottom of page)
Fig. 2.9
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Fig. 2.9
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Fig. 2.9
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FASTA format
Fig. 2.10
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FASTA format
What is an accession number?
An accession number is label that used to identify a
sequence. It is a string of letters and/or numbers that
corresponds to a molecular sequence.
Examples (all for retinol-binding protein, RBP4):
X02775
NT_030059
Rs7079946
GenBank genomic DNA sequence
Genomic contig
dbSNP (single nucleotide polymorphism)
DNA
N91759.1
NM_006744
An expressed sequence tag (1 of 170)
RefSeq DNA sequence (from a transcript)
RNA
NP_007635
AAC02945
Q28369
1KT7
RefSeq protein
GenBank protein
SwissProt protein
Protein Data Bank structure record
protein
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NCBI’s important RefSeq project:
best representative sequences
RefSeq (accessible via the main page of NCBI)
provides an expertly curated accession number that
corresponds to the most stable, agreed-upon “reference”
version of a sequence.
RefSeq identifiers include the following formats:
Complete genome
Complete chromosome
Genomic contig
mRNA (DNA format)
Protein
NC_######
NC_######
NT_######
NM_###### e.g. NM_006744
NP_###### e.g. NP_006735
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NCBI’s RefSeq project: accession for
genomic, mRNA, protein sequences
Accession
AP_123456
NC_123456
NG_123456
NM_123456
NM_123456789
NP_123456
NP_123456789
NR_123456
NT_123456
NW_123456
NZ_ABCD12345678
XM_123456
XP_123456
XR_123456
YP_123456
ZP_12345678
Molecule
Protein
Genomic
Genomic
mRNA
mRNA
Protein
Protein
RNA
Genomic
Genomic
Genomic
mRNA
Protein
RNA
Protein
Protein
Note
Protein products; alternate
Complete genomic molecules
Incomplete genomic regions
Transcript products; mRNA
Transcript products; 9-digit
Protein products;
Protein products; 9-digit
Non-coding transcripts
Genomic assemblies
Genomic assemblies
Whole genome shotgun data
Transcript products
Protein products
Transcript products
Protein products
Protein products
Ensembl to access protein and DNA sequences
Try Ensembl at www.ensembl.org for a premier
human genome web browser.
Ensembl is a joint scientific project between the
European Bioinformatics Institute and the
Wellcome Trust Sanger Institute,
Its aim is to provide a centralised resource for geneticists,
molecular biologists and other researchers studying the
genomes of our own species and other vertebrates.
We will encounter Ensembl as we study the human genome,
BLAST, and other topics.
click
human
Species in Ensembl
MAMMALS
PLACENTALS
MONOTREMES
MARSUPIALS
OTHER BIRDS
BIRDS
REPTILES
PALEOGNATHS
PASSERINES
CROCODILES
TURTLES
LIZARDS
AMPHIBIANS
TELEOSTS
FISHES
SHARKS
RAYS
LATIMERIA
BICHIR/POLYPTERUS
LUNGFISHES
AGNATHANS
NON-VERTEBRATES
enter
RBP4
Five ways to access DNA and
protein sequences
[1] Entrez Gene with RefSeq
[2] UniGene
[3] European Bioinformatics Institute (EBI)
and Ensembl (separate from NCBI)
[4] ExPASy Sequence Retrieval System
(separate from NCBI)
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ExPASy to access protein and DNA sequences
ExPASy sequence retrieval system
(ExPASy = Expert Protein Analysis System)
Visit http://www.expasy.ch/
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Fig. 2.11
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Example of how to access sequence data:
HIV-1 pol
There are many possible approaches. Begin at the main
page of NCBI, and type an Entrez query: hiv-1 pol
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Searching for HIV-1 pol:
Following the “genome” link yields
a manageable three results
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Example of how to access sequence data:
HIV-1 pol
For the Entrez query: hiv-1 pol
there are about 40,000 nucleotide or protein records
(and >100,000 records for a search for “hiv-1”),
but these can easily be reduced in two easy steps:
--specify the organism, e.g. hiv-1[organism]
--limit the output to RefSeq!
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over 100,000
nucleotide entries
for HIV-1
only 1 RefSeq
Examples of how to access sequence data:
histone
query for “histone”
# results
protein records
RefSeq entries
21847
7544
RefSeq (limit to human)
NOT deacetylase
1108
697
At this point, select a reasonable candidate (e.g.
histone 2, H4) and follow its link to Entrez Gene.
There, you can confirm you have the right gene/protein.
8-12-06
Access to Biomedical Literature
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PubMed at NCBI
to find literature
information
PubMed is the NCBI gateway to MEDLINE.
MEDLINE contains bibliographic citations
and author abstracts from over 4,600 journals
published in the United States and in 70 foreign
countries.
It has >14 million records dating back to 1966.
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PubMed search strategies
Try the tutorial (“education” on the left sidebar)
Use boolean queries (capitalize AND, OR, NOT)
lipocalin AND disease
Try using “limits”
Try “Links” to find Entrez information and external resources
Obtain articles on-line via Welch Medical Library
(and download pdf files):
http://www.welch.jhu.edu/
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1 AND 2
1
2
lipocalin AND disease
(60 results)
1 OR 2
1
2
lipocalin OR disease
(1,650,000 results)
1 NOT 2
1
2
lipocalin NOT disease
(530 results)
Fig. 2.12
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8/04