Download Bioinformatic Databases - FAU College of Engineering

COT 6930
HPC and Bioinformatics
Bioinformatics Resources and
Databases
Xingquan Zhu
Dept. of Computer Science and Engineering
Protein
structure
databases
Gene expression
database
transcription
DNA
Genomic
DNA
Databases
translation
RNA
cDNA
ESTs
UniGene
protein
Protein
sequence
databases
phenotype
Gene
Different transcripts can be related
to the same gene!
EST
Expressed Sequence Tags
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Partial copies of mRNA found within a particular
cell
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Can be used to identify genitc regions; splicing
patterns of genes; etc
Outline
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Bioinformatics Databases
 Primary databases
 Derived databases
Nucleotide databases
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GenBank (P), EMBL-Bank (P)
Protein databases
 Swiss-Prot (D), PIR-PSD (D)
 GenPept (D), TrEMBL (D)
 Protein Data Bank (P)
Other Examples
 RefSeq
 UniGene
 PubMed
 SNP
 OMIM
Bioinformatics Databases
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Information
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DNA sequences
Conserved DNA domains
Genomes
Gene expression (ESTs, microarrays)
Protein sequences
Protein 3D structure
Protein families
Mutations / polymorphisms / SNPs
Metabolic pathways
Chemical compounds (ligands)
Biomedical literature (journal papers, online books…)
Primary public domain
bioinformatics servers
Public Domain
Bioinformatics
Facilities
National Center
For Biotechnology
Information (NCBI)
United States
Databases
Analysis
Tools
European Bioinformatics
Institute (EBI)
United Kingdom
Databases
Analysis
Tools
Genome
Net
(KEGG & DDBJ)
Japan
Databases
Analysis
Tools
Major Databases
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DNA sequences
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Protein sequences
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Protein Data Bank (PDB)
Gene expression
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Swiss-Prot, PIR-PSD, GenPept, TrEMBL, RefSeq
Protein structure
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GenBank, RefSeq, UniGene
Gene Expression Omnibus (GEO)
Biomedical publications
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PubMed / MedLine
Bioinformatics Data Sources
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Primary databases
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Original submissions by researchers
Staff organizes information only
Generally sequence oriented
Examples
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GenBank, PDB (Protein Data Bank)
Bioinformatics Data Sources
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Derived databases
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Compiled from data in primary databases
Manually curated (human selection & correction)
 Advantages – high quality
 Disadvantages – high expense, low volume
 Examples
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Swiss-Prot, PIR-PSD, RefSeq
Computational derivation (automatically generated)
 Advantages – inexpensive, up-to-date
 Disadvantages – lower quality
 Examples
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GenPept, TrEMBL, UniGene
Outline
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Bioinformatics Databases
 Primary databases
 Derived databases
Nucleotide databases
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GenBank (P), EMBL-Bank (P)
Protein databases
 Swiss-Prot (D), PIR-PSD (D)
 GenPept (D), TrEMBL (D)
 Protein Data Bank (P)
Other Examples
 RefSeq
 UniGene
 PubMed
 SNP
 OMIM
Bioinformatic Databases –
GenBank
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“GenBank is the NIH genetic sequence database, an annotated
collection of all publicly available DNA sequences”
Database type
 Nucleotide sequences
 Primary database
Current Size (As of Aug. 2006):
 65,369,091,950 (bps)
 61,132,599 (sequences)
Access to GenBank
 Available for searching at NCBI via several methods
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Such as BLAST search
http://www.ncbi.nlm.nih.gov/Genbank/
Bioinformatic Databases – GenBank
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Types of submissions to database
 Genomic DNA
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mRNA / cDNA
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High quality complete DNA sequence
Partial or complete mRNA (or cDNA)
Expressed sequence tag (EST)
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A short sub-sequence of a transcribed spliced nucleotide sequence (mRNA)
(500-800bps)
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Sequence tagged sites (STS)
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Short DNA sequences unique in genome
Genomic survey sequence (GSS)
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May represent portions of expressed genes
Either protein-coding or not
About 43 million ESTs are now available
Single-pass genomic DNA
Third-party annotations of GenBank sequences
Bioinformatic Databases –
EMBL-Bank
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Europe's primary nucleotide sequence resource
Primary databases
Database type
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Nucleotide sequences
Primary database
http://www.ebi.ac.uk/embl/
Outline
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Bioinformatics Databases
 Primary databases
 Derived databases
Nucleotide databases
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GenBank (P), EMBL-Bank (P)
Protein databases
 Swiss-Prot (D), PIR-PSD (D)
 GenPept (D), TrEMBL (D)
 Protein Data Bank (P)
Other Examples
 RefSeq
 UniGene
 PubMed
 SNP
 OMIM
Bioinformatic Databases –
Proteins
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Protein sequence databases
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Once derived from laboratory experiments
Now mostly based on predicted ORFs from DNA
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Manual curation
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Swiss-Prot
PIR-PSD
Computational derivation
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GenPept
TrEMBL
Bioinformatic Databases – SwissProt, PIR-PSD
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Database type
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Many annotations
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Protein sequences
Derived database
 Manually curated (non-redundant, annotated)
Functions of the protein
Domains and sites
Secondary & quaternary structure
Similarities to other proteins
Variants
Swiss-Prot
http://ca.expasy.org/sprot/
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PIR-PSD
http://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml
Bioinformatic Databases –
GenPept, TrEMBL
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Database type
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GenPept
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Protein sequences
Computationally derived database
Predicted (translating) coding sequences (CDS) from GenBank,
EMBL (i.e., gene product)
Download: ftp://ftp.ncifcrf.gov/pub/genpept/
Release 163 (as of 12/26/2007)
 4,970,178 loci containing 1,517,599,916 residues
TrEMBL
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http://www.ebi.ac.uk/trembl/index.html
Structure Databases
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3-dimensional structures of proteins, nucleic
acids, molecular complexes etc
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3-d data is available due to techniques such as NMR
and X-Ray crystallography
Protein Data Bank
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Protein 3D structures
Primary database
(http://www.rcsb.org/pdb/home/home.do)
Protein Data Bank: PDB
Bioinformatic Databases –
Connections
Outline
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Bioinformatics Databases
 Primary databases
 Derived databases
Nucleotide databases
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GenBank (P), EMBL-Bank (P)
Protein databases
 Swiss-Prot (D), PIR-PSD (D)
 GenPept (D), TrEMBL (D)
 Protein Data Bank (P)
Other Examples
 RefSeq
 UniGene
 PubMed
 SNP
 OMIM
Bioinformatic Databases – RefSeq
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The Reference Sequence (RefSeq) collection aims to provide a
comprehensive, integrated, non-redundant set of sequences, including
genomic DNA, transcript (RNA), and protein products.
 Information derived from GenBank records
Database type
 Nucleotide & protein sequences
 Derived database
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Human curated (non-redundant, cross-linked)
Data in RefSeq
 Genomic DNA
 mRNAs & proteins for known genes, gene models
 Entire chromosomes
 Multiple organisms
http://www.ncbi.nlm.nih.gov/projects/RefSeq/
Example
 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_015325
Bioinformatic Databases – UniGene
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UniGene is an experimental system for automatically partitioning
GenBank sequences into a non-redundant set of gene-oriented clusters
Each UniGene cluster contains sequences that represent a unique gene,
as well as related information such as the tissue types in which the gene
has been expressed and map location
Database type
 Nucleotide sequences
 Computationally derived database
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Gene-oriented view
Data in UniGene
 Clusters of genomic DNA & ESTs
 Multiple organisms
http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene
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Partitioned into non-redundant gene-oriented clusters
Bioinformatic Databases – PubMed
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Database type
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Biomedical papers
Manually curated database
Service of the National Library of Medicine
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MEDLINE publication database
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Over 17,000 journals
15 million citations since 1950
http://www.ncbi.nlm.nih.gov/PubMed/
Bioinformatic Databases – Others
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Gene expression
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Multi-organism genomes
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dbSNP, OMIM, CGAP
Metabolic pathways
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Entrez Genome, HomoloGene, COGs, TIGR
Genetic variation & genetic diseases
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ArrayExpress, Gene Expression Omnibus (GEO)
WIT, KEGG
Many more…
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Listed in journal “Nucleic Acids Research” each January
Bioinformatic Databases: SNP
Database
Single Nucleotide Polymorphisms (SNPs)
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Single base difference in a single position among
two different individuals of the same species
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Play an important role in differentiation and
disease
http://www.ncbi.nlm.nih.gov/projects/SNP/
Sickle Cell Anemia
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Due to 1 swapping an A for a T, causing inserted amino acid to be
valine instead of glutamine in hemoglobin
Image source: http://www.cc.nih.gov/ccc/ccnews/nov99/
Healthy Individual
>gi|28302128|ref|NM_000518.4| Homo sapiens hemoglobin, beta (HBB), mRNA
ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGA
GGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGC
AGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATG
CTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGC
TCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGAT
CCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCA
CCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCA
CTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACT
GGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC
>gi|4504349|ref|NP_000509.1| beta globin [Homo sapiens]
MVHLTP
EEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG
AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN
ALAHKYH
Diseased Individual
>gi|28302128|ref|NM_000518.4| Homo sapiens hemoglobin, beta (HBB), mRNA
ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGA
GGTGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGC
AGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATG
CTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGC
TCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGAT
CCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCA
CCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCA
CTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACT
GGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC
>gi|4504349|ref|NP_000509.1| beta globin [Homo sapiens]
MVHLTP
VEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG
AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN
ALAHKYH
Disease Databases
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Genes are involved in disease
Many diseases are well studied
Description of diseases and what is known about them is
stored
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A good place to start when you want to know about a certain
disease
Linked to PubMed, the OMIM Morbid Map
OMIM - Online Mendelian Inheritance in Man
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“A catalog of human genes and genetic disorders maintained by
Johns Hopkins University”
http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim
Putting it All Together
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Each Database contains specific information
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Like other biological systems also these databases
are interrelated
PROTEIN
PIR
DISEASE
ASSEMBLED
GENOMES
LocusLink
SWISS-PROT
OMIM
GoldenPath
OMIA
WormBase
MOTIFS
TIGR
BLOCKS
Pfam
GENOMIC DATA
Prosite
GenBank
ESTs
dbEST
DDBJ
GENES
EMBL
RefSeq
unigene
AllGenes
SNPs
GENE
EXPRESSION
dbSNP
STRUCTURE
PDB
MMDB
SCOP
PATHWAY
Stanford MGDB
KEGG
NetAffx
COG
ArrayExpress
GDB
LITERATURE
PubMed
Where to get started? NCBI ENTREZ
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A search engine that provides access and links between
various databases
ENTREZ
PubMed
GenBank
Protein Genomes
databases
SNP
http://www.ncbi.nlm.nih.gov/sites/gquery
Taxonomy
OMIM
Outline
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Bioinformatics Databases
 Primary databases
 Derived databases
Nucleotide databases
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GenBank (P), EMBL-Bank (P)
Protein databases
 Swiss-Prot (D), PIR-PSD (D)
 GenPept (D), TrEMBL (D)
 Protein Data Bank (P)
Other Examples
 RefSeq
 UniGene
 PubMed
 SNP
 OMIM