Biological Databases

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Biological Databases

• Bioinformatics Databases for the Molecular
  Biologist 8.9.2003
• Lorenza Bordoli

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Overview

• Introduction to Biological Databases
• Sequences DNA and Protein
• Species Specific (Genomics)
• Protein families and domains
• Mutation and polymorphisms
• Proteomics
• 3D structures
• Conclusions

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Introduction
4
What is a database ?

• A collection of
• structured
• searchable (index) -gt table of contents
• updated periodically (release) -gt new edition
• cross-referenced (hyperlinks) -gt links with
  other db
• data
• Includes also associated tools (software)
  necessary for db access/query, db updating, db
  information insertion, db information deletion.
• Data storage/ressource management
• flat files, relational databases, objet
  oriented, )

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Why biological databases ?

• Exponential growth in biological data.
• Data (genomic sequences, 3D structures, 2D gel
  analysis, MS analysis, Microarrays.) are no
  longer published in a conventional manner, but
  directly submitted to databases.
• Essential tools for biological research.

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Some statistics

• More than 1000 different biological databases
• Variable size lt100Kb to gt10Gb
• DNA gt 10 Gb
• Protein 1 Gb
• 3D structure 5 Gb
• Other smaller
• Update frequency daily to annually
• Usually accessible through the web (free !?)
• Amos links www.expasy.org/alinks.html
• Biohunt http//www.expasy.org/BioHunt/
• Google http//www.google.com/

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ExPASy Server
ExPASy Web Server ExPASy Expert Protein
Analysis System
http//www.expasy.org/
8

• Some databases in the field of molecular
  biology
• AATDB, AceDb, ACUTS, ADB, AFDB, AGIS, AMSdb,
• ARR, AsDb, BBDB, BCGD, Beanref,
  Biolmage,
• BioMagResBank, BIOMDB, BLOCKS,
  BovGBASE,
• BOVMAP, BSORF, BTKbase, CANSITE, CarbBank,
• CARBHYD, CATH, CAZY, CCDC, CD4OLbase, CGAP,
• ChickGBASE, Colibri, COPE, CottonDB, CSNDB, CUTG,
• CyanoBase, dbCFC, dbEST, dbSTS, DDBJ, DGP,
  DictyDb,
• Picty_cDB, DIP, DOGS, DOMO, DPD, DPlnteract,
  ECDC,
• ECGC, EC02DBASE, EcoCyc, EcoGene, EMBL, EMD db,
• ENZYME, EPD, EpoDB, ESTHER, FlyBase, FlyView,
• GCRDB, GDB, GENATLAS, Genbank, GeneCards,
• Genline, GenLink, GENOTK, GenProtEC,
  GIFTS,
• GPCRDB, GRAP, GRBase, gRNAsdb, GRR, GSDB,
• HAEMB, HAMSTERS, HEART-2DPAGE, HEXAdb, HGMD,
• HIDB, HIDC, HlVdb, HotMolecBase, HOVERGEN, HPDB,
• HSC-2DPAGE, ICN, ICTVDB, IL2RGbase, IMGT, Kabat,
• KDNA, KEGG, Klotho, LGIC, MAD, MaizeDb, MDB,

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Categories of databases for Life Sciences

• Sequences (DNA, protein) (primary db)
• Genomics (Species Specific)
• Mutation/polymorphism
• Protein domain/family (----gt tools)
• Proteomics (2D gel, Mass Spectrometry)
• 3D structure
• Metabolism
• Bibliography
• Others (Microarrays, Protein protein
  interaction)

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Sequence Databases

• DNA/RNA
• Protein

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Ideal minimal content of a sequence database entry

• Sequences !!
• Accession number (AC) (unique identifier)
• Taxonomic data
• References
• ANNOTATION/CURATION (gt not always the case !)
• Keywords
• Cross-references
• Documentation

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Sequence database example
SWISS-PROT (protein db) (flat file)
Accession number
Taxonomy
Reference
Annotations (comments)
Cross-references
Keywords
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Sequence database example (cont.)
Annotations (features)
Sequence
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Sequence Databases

• DNA/RNA

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Sequence Database 1. nucleotide sequences

• The 3 main nucleic acid sequence databases (DNA)
  are
• EMBL (Europe)/GenBank (USA) /DDBJ (Japan)
• EMBL since 1982
• Specialized databases for the different types of
  RNAs (i.e tRNA, rRNA, tmRNA, URNA,)
• 3D structure (DNA and RNA)-gtPDB
• Others Aberrant splicing db, Eukaryotic promoter
  db (EPD) RNA editing sites, Multimedia Telomere
  Resource,

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Nucleotids and associated topics databases
(AMOSlinks) EMBL - EMBL Nucleotide
sequence db (EBI) Genbank - GenBank
Nucleotide Sequence db (NCBI) DDBJ - DNA
Data Bank of Japan dbEST - dbEST
(Expressed Sequence Tags) db (NCBI) dbSTS
- dbSTS (Sequence Tagged Sites) db (NCBI)
NDB - Nucleic Acid Databank (3D structures)
BNASDB - Nucleic acid structure db from
University of Pune AsDb - Aberrant
Splicing db ACUTS - Ancient conserved
untranslated DNA sequences db Codon Usage
Db EPD - Eukaryotic Promoter db
HOVERGEN - Homologous Vertebrate Genes db
IMGT - ImMunoGeneTics db Mirror at EBI
ISIS - Intron Sequence and Information System
RDP - Ribosomal db Project gRNAs db -
Guide RNA db PLACE - Plant cis-acting
regulatory DNA elements db PlantCARE -
Plant cis-acting regulatory DNA elements db
sRNA db - Small RNA db ssu rRNA - Small
ribosomal subunit db lsu rRNA - Large
ribosomal subunit db 5S rRNA - 5S
ribosomal RNA db tmRNA Website
tmRDB - tmRNA dB tRNA - tRNA compilation
from the University of Bayreuth uRNADB -
uRNA db RNA editing - RNA editing site
RNAmod db - RNA modification db
SOS-DGBD - Db of Drosophila DNA sequences
annotated with regulatory binding sites
TelDB - Multimedia Telomere Resource
TRADAT - TRAnscription Databases and Analysis
Tools Subviral RNA db - Small circular
RNAs db (viroid and viroid-like) MPDB -
Molecular probe db OPD - Oligonucleotide
probe db VectorDB - Vector sequence db
(seems dead!)
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Sequence Database 1. DNA EMBL/GenBank/DDBJ

• These 3 db contain mainly the same informations
  within 2-3 days (few differences in the format
  and syntax)
• Contribution EMBL 10 GenBank 73 DDBJ 17
• Serve as archives containing all sequences
  (single genes, ESTs, complete genomes, etc.)
  derived from
• Genome projects (gt 80 of entries)
• Sequencing centers
• Individual scientists ( 15 of entries)
• Patent offices (i.e. European Patent Office, EPO)
• Currently 18 x106 sequences, 30 x109 bp
• Sequences from gt 50000 different species

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The tremendous increase in nucleotide sequences
EMBL datafirst increase in data due to the PCR
development
human
High throughput genomes (HTG)
mouse
rat
human
1980 80 genes fully sequenced !
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EMBL/GenBank/DDBJ

• Heterogeneous sequence qualities and length
  ESTs, genomes, variants, fragments
• Sequence sizes
• max 350000 bp /entry (! genomic sequences,
  overlapping)
• min 10 bp /entry
• Archive nothing goes out -gt highly redundant !
• full of errors in sequences, in annotations, in
  CDS attribution.
• no consistency of annotations most annotations
  are done by the submitters heterogeneity of the
  quality and the completion and updating of the
  informations
• entries contain only the assembly data

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EMBL/GenBank/DDBJ

• Unexpected information you can find in these db
• FT source 1..124
• FT /db_xref"taxon4097"
• FT /organelle"plastidchloropla
  st"
• FT /organism"Nicotiana
  tabacum"
• FT /isolate"Cuban cahibo
  cigar, gift from President Fidel
• FT Castro"
• Or
• FT source 1..17084
• FT /chromosome"complete
  mitochondrial genome"
• FT /db_xref"taxon9267"
• FT /organelle"mitochondrion"
• FT /organism"Didelphis
  virginiana"
• FT /dev_stage"adult"
• FT /isolate"fresh road killed
  individual"
• FT /tissue_type"liver"

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EMBL entry example

• ID HSERPG standard DNA HUM 3398 BP.
• XX
• AC X02158
• XX
• SV X02158.1
• XX
• DT 13-JUN-1985 (Rel. 06, Created)
• DT 22-JUN-1993 (Rel. 36, Last updated, Version
  2)
• XX
• DE Human gene for erythropoietin
• XX
• KW erythropoietin glycoprotein hormone
  hormone signal peptide.
• XX
• OS Homo sapiens (human)
• OC Eukaryota Metazoa Chordata Craniata
  Vertebrata Euteleostomi Mammalia
• OC Eutheria Primates Catarrhini Hominidae
  Homo.
• XX
• RN 1
• RP 1-3398

keyword
taxonomy
references
Cross-references
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EMBL entry (cont.)

• CC Data kindly reviewed (24-FEB-1986) by K.
  Jacobs
• FH Key Location/Qualifiers
• FH
• FT source 1..3398
• FT /db_xreftaxon9606
• FT /organismHomo sapiens
• FT mRNA join(397..627,1194..1339,1596
  ..1682,2294..2473,2608..3327)
• FT CDS join(615..627,1194..1339,1596
  ..1682,2294..2473,2608..2763)
• FT /db_xrefSWISS-PROTP01588
• FT /producterythropoietin
• FT /protein_idCAA26095.1
• FT /translationMGVHECPAWLWLLLSL
  LSLPLGLPVLGAPPRLICDSRVLQRYLLE
• FT AKEAENITTGCAEHCSLNENITVPDTKVN
  FYAWKRMEVGQQAVEVWQGLALLSEAVLRG
• FT QALLVNSSQPWEPLQLHVDKAVSGLRSLT
  TLLRALGAQKEAISPPDAASAAPLRTITAD
• FT TFRKLFRVYSNFLRGKLKLYTGEACRTGD
  R
• FT mat_peptide join(1262..1339,1596..1682,22
  94..2473,2608..2763)
• FT /producterythropoietin
• FT sig_peptide join(615..627,1194..1261)
• FT exon 397..627

CDS Coding sequence
annotation
sequence
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EMBL The Genome divisionshttp//www.ebi.ac.uk/ge
nomes/
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Nucleotide databases and  associated  genomic
projects/databases

• Problem
• Redundancy makes Blasts searches of the
  complete
• databases useless for detecting anything behond
  the closest homologs.
• Solutions
• assemblies of genomic sequence data (contigs)
  and corresponding RNA and
• protein sequences -gt dataset of genomic contigs,
  RNAs and proteins
• annotation of genes, RNAs, proteins, variation
  (SNPs), STS markers,
• gene prediction, nomenclature and chromosomal
  location.
• compute connection to other resources
  (cross-references)
• Examples RefSeq/Locus link (drosophila, human,
  mouse, rat and zebrafish),
• TIGR (bacteria and plants),
  Ensembl (Eukaryota)

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Nucleotide databases and  associated  genomic
projects/databases

• LocusLink (http//www.ncbi.nlm.nih.gov/LocusLink/
  )
• Focal point for genes and associated
  information (C. elegans, cow, fruit fly, human,
  human HIV type 1, mouse, rat and zebrafish)
• RefSeq
• Reference mRNAs and proteins for
  human, mouse, rat
• UniGene
• UniGene clusters, expression data
• Ensembl
• Provides a bioinformatics framework to organise
  biology around the sequences of large genomes.
  Available now are human, mouse, rat,fugu,
  zebrafish, mosquito, Drosophila, C. elegans, and
  C. briggsae,

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Nucleotide databases and  associated  genomic
projects/databases

• LocusLink
• From gene loci to curated sequences and
  descriptive informations.

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LocusLink
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LocusLink
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Nucleotide databases and  associated  genomic
projects/databases

• RefSeq Reference sequences of genomic contigs,
  mRNAs, and proteins.

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Nucleotide databases and  associated  genomic
projects/databases

• UniGene 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.

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Nucleotide databases and  associated  genomic
projects/databases

• Ensembl Provides a bioinformatics framework to
  organise biology around the sequences of large
  genomes. Available now are human, mouse,
  rat,fugu, zebrafish, mosquito, Drosophila, C.
  elegans, and C. briggsae,

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Sequence Databases

• 2. Protein

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Sequence Database 2. Proteins

• SWISS-PROT created in 1986 (A.Bairoch)
  http//www.expasy.org/sprot/
• TrEMBL created in 1996 complement to
  SWISS-PROT derived from EMBL CDS translations
  ( proteomic  version of EMBL)
• PIR-PSD Protein Information Resources
  http//pir.georgetown.edu/
• Genpept  proteomic  version of GenBank
• Many specialized protein databases for specific
  families or groups of proteins (M. Primig)
• Examples AMSDb (antibacterial peptides), GPCRDB
  (7 TM receptors), IMGT (immune system) YPD
  (Yeast),

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The first protein db
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Swiss-Prot

• Collaboration between the SIB (Geneva) and
  EMBL/EBI (UK)
• Fully manually annotated, non-redundant,
  cross-referenced, documented protein sequence
  database.
• 113 000 sequences from more than 6800
  different species 70 000 references
  (publications) 550 000 cross-references
  (databases) 200 Mb of annotations
• Weekly releases available from about 50 servers
  across the world, the main source being ExPASy

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TrEMBL (Translation of EMBL)

• It is impossible to cope with the quantity of
  newly generated data AND to maintain the high
  quality of SWISS-PROT -gt TrEMBL, created in 1996.
• TrEMBL is automatically generated (from annotated
  EMBL coding sequences (CDS)) and annotated using
  software tools.
• Contains all what is not in SWISS-PROT.
• SWISS-PROT TrEMBL all known protein
  sequences.
• Well-structured SWISS-PROT-like resource.

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The simplified story of a Swiss-Prot entry
Some data are not submitted to the public
databases !! (delayed or cancelled)
cDNAs, genomes,

•  Automated 
• Redundancy check (merge)
• Family attribution (InterPro)
• Annotation (computer)

EMBLnew EMBL
CDS
TrEMBLnew TrEMBL

•  Manual 
• Redundancy (merge, conflicts)
• Annotation (manual)
• Swiss-Prot tools (macros)
• Swiss-Prot documentation
• Medline
• Databases (MIM, MGD.)
• Brain storming

Swiss-Prot
Once in Swiss-Prot, the entry is no more in
TrEMBL, but still in EMBL (archive)
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Some nomenclature Example SRS6 at the Sanger
Center
http//www.sanger.ac.uk/srs6bin/cgi-bin/wgetz?-pag
etop
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SWISS-PROT (SP)TrEMBL TrEMBL new (SWALL,
SPTR) (Standard)
(Preliminary)

• TrEMBL SPTrEMBL REMTrEMBL
• SPTrEMBL contains TrEMBL entries which will be
  integrated into SWISS-PROT.
• REMTrEMBL contains TrEMBL entries which will
  never be integrated into SWISS-PROT
  (Immunoglobulins and T-cell receptors, Synthetic
  sequences, Patent application sequences
• Small fragments, CDS not coding for real
  proteins)
• TrEMBLnew contains entries which have not yet
  been integrated into TrEMBL (weekly update to
  TrEMBL)
• SPTR (SWall) SWISS-PROT (SP)TrEMBL
  TrEMBLnew
• ! Usually what we call TrEMBL is (SP)TrEMBL and
  does not include REMTrEMBL !

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a Swiss-Prot entry overview
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Protein name Gene name
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Cross-references
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Keywords
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TrEMBL example
Original TrEMBL entry which has been integrated
into the SWISS-PROT EPO_HUMAN entry and thus
which is not found in TrEMBL anymore.
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Swiss-Prot / TrEMBL a minimal of redundancy

• Swiss-Prot and TrEMBL introduces some degree of
• redundancy
• Only 100 identical sequences are automatically
  merged
• between SWISS-PROT and TrEMBL
• Complete sequences or fragments with 1-3
  conflicts will be
• automatically merged soon (genome projects check
  for chromosomal location and gene names)

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Swiss-Prot / TrEMBL a minimal of redundancy
Human EPO Blastp results
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Swiss-Prot and the cross-references (X-ref)

• SWISS-PROT was the 1st database with X-ref.
• Explicitly X-referenced to 36 databases
• X-ref to DNA (EMBL/GenBank/DDBJ), 3D-structure
  (PDB),
• literature (Medline), genomic (MIM, MGD,
  FlyBase, SGD, SubtiList,
• etc.), 2D-gel (SWISS-2DPAGE), specialized db
  (PROSITE,
• TRANSFAC)
• Implicitly X-referenced to 17 additional db
  added by the ExPASy
• servers on the WWW (i.e. GeneCards, PRODOM,
  HUGE, etc.)
• Gasteiger et al., Curr. Issues Mol. Biol.
  (2001), 3(3) 47-55

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Domains, functional sites, protein
families PROSITE InterPro Pfam PRINTS SMART Mendel
-GFDb
Human diseases MIM
Protein-specific dbs GCRDb MEROPS REBASE TRANSFAC
2D and 3D Structural dbs HSSP PDB
Organism-spec. dbs DictyDb EcoGene FlyBase HIV Mai
zeDB MGD SGD StyGene SubtiList TIGR TubercuList Wo
rmPep Zebrafish
Swiss-Prot
PTM CarbBank GlycoSuiteDB
2D-gel protein databases SWISS-2DPAGE ECO2DBASE HS
C-2DPAGE Aarhus and Ghent MAIZE-2DPAGE
Nucleotide sequence db EMBL, GeneBank, DDBJ
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• http//pir.georgetown.edu/

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• UniProt
• United Protein database
• Swiss-Prot TrEMBL PIR
• Born in oct 2002
• NIH pledges cash for global protein database
  The United States is turning to European
  bioinformatics facilities to help it meet
• its researchers' future needs for databases of
  protein sequences.European institutions are set
  to be the main recipients of a 15-million,
• three-year grant from the US National Institutes
  of Health (NIH), to set up
• a global database of information on protein
  sequence and function known as the
• United Protein Databases, or UniProt (Nature,
  419, 101 (2002))

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Species Specific Databases
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Species Specific Databases

• Contain information on gene chromosomal location
  (mapping) and nomenclature, and provide links to
  sequence databases usually do not contain
  sequence (but crosslink to it)
• all species whose genome has been sequenced,
  annotated and published come with their own
  species genome database that enables scientists
  to retrieve information about DNA and it's gene
  products (see also NAR Database issue 2003 at
  http//nar.oupjournals.org/content/vol31/issue1/
  and the new NAR Web server Issue 2003 at
  http//nar.oupjournals.org/content/vol31/issue13)
  
• AMOS links http//www.expasy.org/alinks.htmlOrg
  anisms
• species specific db session

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Species Specific DBs examples

• Human
• GDB The Genome Database is the official central
  repository for genomic mapping data resulting
  from the Human Genome Initiative. Although GDB
  has historically focused on gene mapping, as the
  Genome Project moves from mapping to sequence to
  functional analysis, GDB's focus will be
  broadened. Extensions are under development in
  the representation of sequence-level genome
  content, including sequence variations, along
  with richer descriptions of function and
  phenotype.
• GeneCards - Db integrating information on human
  genes
• GeneLynx - Portal to the human genome

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GeneCards
an electronic encyclopedia of biological and
medical information
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Gene Lynx
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Gene Lynx
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Species Specific DBs examples

• Mouse
• MGI Mouse Genome Informatics provides
  integrated access to data on the genetics,
  genomics, and biology of the laboratory mouse
• C.elegans
• WormBase WormBase is an international consortium
  of biologists and computer scientists dedicated
  to providing the research community with
  accurate, current, accessible information
  concerning the genetics, genomics and biology of
  C. elegans and some related nematodes.
• Yeast
• SGD database of the molecular biology and
  genetics of the yeast Saccharomyces cerevisiae
• Arabidopsis
• TAIR The Arabidopsis Information Resource
  provides a comprehensive resource for the
  scientific community working with Arabidopsis
  thaliana, a widely used model plant. TAIR
  consists of a searchable relational database,
  which includes many different datatypes.
• Drosophila
• The Flybase FlyBase is a database of genetic
  and molecular data for Drosophila. FlyBase
  includes data on all species from the family
  Drosophilidae the primary species represented is
  Drosophila melanogaster.

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Protein families domains DB
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Protein families domains DB

• Most proteins have  modular  structures
• Estimation 3 domains / protein
• Motifs conserved regions within a domain, can be
  identified by multiple sequence alignments
• Protein motifs can be defined by different
  methods (descriptors)
• Pattern
• Profiles
• HMMs

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Protein families domains DB

• Contains biologically significant motifs
  descriptors  (pattern / profiles/ HMM) formulated
  in such a way that, with appropriate computional
  tools, it can rapidly and reliably determine to
  which known family of proteins (if any) a new
  sequence belongs to.
• Used as a tool to identify the function of
  uncharacterized proteins translated from genomic
  or cDNA sequences ( functional diagnostic )
• Either manually curated (i.e. PROSITE, Pfam,
  etc.) or automatically generated (i.e. ProDom,
  DOMO)

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Protein families domains DB
Interpro
PROSITE Patterns / Profiles ProDom Aligned
motifs (PSI-BLAST) (Pfam B) PRINTS Aligned
motifs Pfam HMM (Hidden Markov Models)
SMART HMM TIGRfam HMM DOMO Aligned
motifs BLOCKS Aligned motifs (PSI-BLAST) CDD(CDAR
T) PSI-BLAST(PSSM) of Pfam and SMART
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Protein families domains DB PROSITE

• Contains functional domains fully annotated,
  based on two methods patterns and profiles
• Entries are deposited in PROSITE in two distinct
  files
• Pattern/profiles with the list of all matches in
  Swiss-Prot
• Documentation

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PROSITE Documentation
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PROSITE entry
Diagnostic performance
List of matches
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PROSITE entry
Diagnostic performance
List of matches
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PROSITE access
Search for an entry
Search for the occurrence Of domain in your
protein
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Protein families domains DB Pfam
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Protein families domains DB InterPro

• Composite DB direct access to different protein
  families DBs

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Protein families domains DB InterPro
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Mutations Polymorphisms DB
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Mutations Polymorphisms DB

• Contain informations on sequence variations
  linked or not to genetic diseases
• Mainly human but OMIA - Online Mendelian
  Inheritance in Animals
• General db
• OMIM
• HMGD - Human Gene Mutation db
• SVD - Sequence variation db
• HGBASE - Human Genic Bi-Allelic Sequences db
• dbSNP - Human single nucleotide polymorphism
  (SNP) db
• Disease-specific db most of these databases are
  either linked to a single gene or to a single
  disease
• p53 mutation db
• ADB - Albinism db (Mutations in human genes
  causing albinism)
• Asthma and Allergy gene db

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Mutations Polymorphisms Definitions

• SNPs single nucleotide polymorphisms occur
  approximately once every 100 to 300 bases
• (distinction between sequencing error and
  polymorphism !)
• c-SNPs coding single nucleotide polymorphisms
  (Single Nucleotide Polymorphisms within cDNA
  sequences)
• SAPs single amino-acid polymorphisms
• Missense mutation -gt SAP
• Nonsense mutation -gt STOP
• Insertion/deletion of nucleotides -gt frameshift

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Mutations Polymorphisms DB examples

• OMIM Online Mendelian Inheritance in Man
• catalog of human genes and genetic disorders
• contains a summary of literature and reference
  information. It also contains links to
  publications and sequence information.
• TSC The SNP consortium
• Public/private collaboration Bayer, Roche, IBM,
  Pfizer, Novartis, Motorola
• SNPs dbSNP at NCBI
• Collaboration between the National Human Genome
  Research Institute and the National Center for
  Biotechnology Information (NCBI)
• Chromosome 21 dbSNP
• A joint project between the Division of Medical
  Genetics of the
  University of Geneva Medical School and the SIB

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Mutations Polymorphisms DB

• Generally modest size lack of coordination and
  standards in these databases making it difficult
  to access the data.
• There are initiatives to unify these databases
• SVD Sequence Variation Database project at EBI
  (HMutDB)
• (http//www2.ebi.ac.uk/mutations/)
• HUGO Mutation Database Initiative (MDI).
• Human Genome Variation Society
• (http//www.genomic.unimelb.edu.au/mdi/dblist
  /dblist.html)

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Proteomics DatabasesSWISS-2DPAGE
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Proteomics DB

• Contain informations obtained by 2D-PAGE images
  of master gels and description of identified
  proteins
• Examples SWISS-2DPAGE, ECO2DBASE, Maize-2DPAGE,
  Sub2D, Cyano2DBase, etc.
• Composed of image and text files

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Proteomics DB SWISS-2DPAGE
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Proteomics DB SWISS-2DPAGE
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Proteomics DB SWISS-2DPAGE
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3D structures DatabasesPDB
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3D structures Databases PDB

• Worldwide repository for the processing and
  distribution of 3-D biological macromolecular
  structure data
• Proteins represent more than 90 of available
  structures (others are DNA, RNA, sugars, viruses,
  protein/DNA complexes)
• http//www.pdb.org
• Contains protein structures solved experimentally
  (X-Ray, NMR, EM)
• Provides
• Coordinates (often structure factors, NOEs,
  other experimental data)
• stored as pdb or mmCIF file
• Images
• Links to derived data, e.g. similar structures,
  fold families, etc.

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3D structures Databases PDB

• SHEET 3 S10 PHE 66 PHE 70 -1 O ASN
  67 N LEU 60 12CA 68
• SHEET 4 S10 TYR 88 TRP 97 -1 O PHE
  93 N VAL 68 12CA 69
• SHEET 5 S10 ALA 116 ASN 124 -1 O HIS
  119 N HIS 94 12CA 70
• SHEET 6 S10 LEU 141 VAL 150 -1 O LEU
  144 N LEU 120 12CA 71
• SHEET 7 S10 VAL 207 LEU 212 1 O ILE
  210 N GLY 145 12CA 72
• SHEET 8 S10 TYR 191 GLY 196 -1 O TRP
  192 N VAL 211 12CA 73
• SHEET 9 S10 LYS 257 ALA 258 -1 O LYS
  257 N THR 193 12CA 74
• SHEET 10 S10 LYS 39 TYR 40 1 O LYS
  39 N ALA 258 12CA 75
• TURN 1 T1 GLN 28 VAL 31 TYPE VIB
  (CIS-PRO 30) 12CA 76
• TURN 2 T2 GLY 81 LEU 84 TYPE
  II(PRIME) (GLY 82) 12CA 77
• TURN 3 T3 ALA 134 GLN 137 TYPE I
  (GLN 136) 12CA 78
• TURN 4 T4 GLN 137 GLY 140 TYPE I
  (ASP 139) 12CA 79
• TURN 5 T5 THR 200 LEU 203 TYPE VIA
  (CIS-PRO 202) 12CA 80
• TURN 6 T6 GLY 233 GLU 236 TYPE II
  (GLY 235) 12CA 81
• CRYST1 42.700 41.700 73.000 90.00 104.60
  90.00 P 21 2 12CA 82
• ORIGX1 1.000000 0.000000 0.000000
  0.00000 12CA 83
• ORIGX2 0.000000 1.000000 0.000000
  0.00000 12CA 84
• ORIGX3 0.000000 0.000000 1.000000
  0.00000 12CA 85
• SCALE1 0.023419 0.000000 0.006100
  0.00000 12CA 86

Coordinates of each atom
90
3D structures Databases PDB
91
Conclusions
92
Database retrieval tools

• Query tools associated with the Databases
• Sequence Retrieval System (SRS, Europe) allows
  any flat-file db to be indexed to any other
  allows to formulate queries across a wide range
  of different db types via a single interface,
  without any worry about data structure, query
  languages
• Entrez (NCBI) less flexible than SRS but
  exploits the concept of  neighbouring , which
  allows related articles in different db to be
  linked together, whether or not they are
  cross-referenced directly
• ATLAS specific for macromolecular sequences db
  (i.e. NRL-3D)
• .

93
Where and what ?

• Swiss Institute of Bioinformatics (Geneva,
  Lausanne, Basel)

• Swiss-Prot
• PROSITE
• TrEMBL
• ExPASy server
• EMBnet server BLAST

http//www.isb-sib.ch

• European Bioinformatics Institute (UK/D)

• EMBL
• INTERPRO
• TrEMBL

http//www.ebi.ac.uk/embl/

• National Center for Biotechnology Information
  (USA)

• BLAST
• Genebank
• Lokuslink
• RefSeq

http//www.ncbi.nlm.nih.gov/

• Ensembl
• Pfam

• The Wellcome Trust Sanger Institute (UK)

http//www.sanger.ac.uk/