DATABASE DALAM BIOINFORMATIKA Pengantar Bioinformatika

GENAP TA 2021/2011
DATABASE
Database
Kumpulan informasi terorganisasi –dalam komputer- ‘readable format’
‘structured, searchable, updated, cross referenced’

•Non redundancy
•Contents, list of valid terms and definitions
•The logical structure –schema-
 Flat file database
•Format of the data
 Relational database
•The routes for selective retrieval of data  Object-oriented
•Link to other information sources
DATABASE
Relational database
a set of correspondence between different features of the database content -tables-
RD  data is organized as tables, each table comprising a group of records with the
same fields, allows data to be linked (ex: 2 table properties asam amino protein)
DATABASE
Database berdasarkan sumber:
PRIMER – diperoleh dari lab experimental
SEKUNDER – derived from primary data
DATABASE
Berdasarkan nature of the data primary
nucleotide
secondary

sequence sequence
primary

structure protein secondary

Signal tranduction pathway interaction

Nethpath

Gene expression Ensembl

Metabolic Pathway BRENDA

DATABASE Database

Nucleotide Specialized Whole Genome Protein

OMIM
ENSEMBL
Gene Expression
Omnibus – UniProt
EMBL Microarray Sequence PIR
Genbank SwissProt
DDBJ
Biogrid Protein-protein
ISNDC (International Nucleotide Sequence Database Structure STRING interaction
Collaboration)

PDB 1. Protein databank

Interaction CATH 2. Class, architecture,
SCOPE topology, homology
3. Structural classification
of protein
DATABASE
List of Databases
NAR databases– the most extensive list of biological databases maintained by the
international journal Nucleic Acids Research
http://www.oxfordjournals.org/nar/database/c/
NCBI databases– the molecular databases maintained by NCBI
A Flash flowchart for 24 databases connected by lines shows the relationships and internal
links among all these databases; divided into 6 major groups: nucleotide, protein, structure,
taxonomy, genome, and expression; provides links to the individual database description page
http://www.ncbi.nlm.nih.gov/Database/
EBI databases–divided in several groups: literature, microarray, nucleotide, protein, structure,
pathway, and ontology; provides links to database query and retrieval systems
http://www.ebi.ac.uk/Databases/
DATABASE
Databases Query System
NCBI Entrez– the unique interface to search all NCBI databases
Query results are displayed with entry numbers along the database names
http://www.ncbi.nlm.nih.gov/sites/gquery
EBI SRS - the database query system maintained by EBI
SRS: sequence retrieval system (Etzold, T EMBL 1990s moved to EBI)
http://srs.ebi.ac.uk/
EMBL SRS– the database query system (ver. 8.2) maintained by EMBL, at Germany
http://srs.embl.de/
DATABASE
Databases Query System
DKFZ SRS the database query system (ver. 8.2) maintained by the German
Cancer Research Center
http://www.dkfz-heidelberg.de/srs/
Columbia SRS– the database query system (ver. 8.2) maintained by the Columbis
University
http://walnut.bioc.columbia.edu/srs7
CMBI SRS- the open-source database query system developed by Marteen Hekkelman at
the Center for Molecular and Biomolecular Information (CMBI), the Netherlands
http://mrs.cmbi.ru.nl/mrs-3/
DATABASE
Genome Databases
GOLD - Genomes Online Database, a comprehensive information resource for
complete and on going genome sequencing projects with flowcharts and tables of
statistical data
http://www.genomesonline.org/
Karyn’s Genome - a collection of sequenced genomes with brief description and references for
each genome; provides direct links to the sequence data in EMBL or annotations in ENSEMBL
http://www.ebi.ac.uk/2can/genomes/genomes.html
CropNet - the website of the UK Crop Plant Bioinformatics Network to the development,
management, and distribution of information relating to comparative mapping and genome
research in crop plants
http://ukcrop.net/
DATABASE
Genome Browser and Analysis Platform
NCBI Genome– the entry portal to various NCBI genomic biology tools and resources,
including the Map Viewer, the Genome Project Database, and the Plant Genomes Central
GoldenPath– the genome browser website containing the reference sequence and working
draft assemblies for a large collection of genomes at the University of California at Santa
Cruz (UCSC)
ENSEMBL– the web server of the European eukaryotic genome resource developed by EBI and
the Sanger Institute
VISTA– a comprehensive suite of programs and databases for comparative analysis of
genomic sequences
TIGR Plant Genomics– TIGR plant genome databases and tools
TIGR Gene Indices– TIGR gene indices maintained at Harvard
DATABASE
Genome Database and Model Organism
Gramene – a curated open-source data resource for comparative genome analysisin the
grasses including rice, maize, wheat, barley, and sorghum, as well as other plants including
arabidopsis, poplar, and grape. Cross-species homology relationships can be found using
information derived from genomic and EST sequencing, protein structure and function analysis,
genetic and physical mapping, interpretation of biochemical pathways, gene and QTL
localization, anddescriptions of phenotypic characters and mutations
TA I R– the Arabidopsis information resource maintained by Stanford University. It includes the
complete genome sequence along with gene structure, gene product information, metabolism,
gene expression, DNA and seed stocks, genomemaps, genetic and physical markers,
publications, and information about the Arabidopsis research community
DATABASE
Genome Database and Model Organism
AtENSEMBL– a genome browser for the commonly studied plant modelorganism
Arabidopsis thaliana
Oryzabase– a comprehensive rice science database maintained by the National
Institute of Genetics, Japan. It contains genetic resource stock information, gene
dictionary, chromosome maps, mutant images, and fundamental knowledge ofrice
science
FlyBase– a comprehensive database of Drosophila genes and genomes maintained
by Indiana University
CyanoBase– the genome database for cyanobacteria developed by KazusaInstitute,
Japan
DATABASE
DNA Sequence Databases
GenBank– the web portal to the NIH genetic sequence database maintained by NCBI, also a part of the
International Nucleotide Database Collaboration
EMBL– the web portal to EMBL nucleotide sequence database maintained by EBI, also a part of the
International Nucleotide Database Collaboration
RefSeq– the Reference Sequence collection constructed by NCBI to provide a comprehensive, integrated,
non-redundant set of DNA and RNA sequences and protein products. It provides a stable reference for
genome annotation, gene identification and characterization, mutation and polymorphism analysis,
expression studies, and comparative analyses.
UniGene– an Organized View of the Transcriptome created by NCBI. Each UniGene entry is a set of
transcript sequences that appear to come from the same transcription locus, together with information on
protein similarities, gene expression, cDNA clone reagents, and genomic location.
dbSNP– the database of single nucleotide polymorphism maintained by NCBI.
EMBLCDS– a database of nucleotide sequences of the coding sequence from EMBL
DATABASE
Protein Sequence Databases
Swiss-Prot– the entry site for the well-annotated protein sequence knowledge database
maintained by SIB at Geneva, Switzerland. A list of references, acomprehensive user manual,
and database statistics with tables and flowchartsare provided
UniProt– the main website for international protein sequence database which consists of the
protein knowledgebase (UniProtKB), the sequence clusters (UniRef), and the sequence archive
(UniParc)
HPI– the Human Proteomics Initiative, an EBI project to annotate all known human sequences
according to the quality standards of UniProtKB/Swiss-Prot. It provides for each known protein a
wealth of information that includes the description of its function, its domain structure, subcellular
location, posttranslational modifications, variants, and similarities to other proteins
IPI– the website of the International Protein Index database which provides a toplevel guide to
the main databases that describe the proteomes of higher eukaryotic organisms
DATABASE
Protein Domain Databases
Prosite– a database of protein domains, families, and functional sites, created and maintained
by the Swiss Institute of Bioinformatics
PRINTS– a database of protein fingerprints consisting of conserved motifs within a protein
family, created and maintained by Manchester University, UK
BLOCKS– a database of multiple aligned ungapped segments corresponding to the most highly
conserved regions of proteins, created and maintained by the Fred Hutchinson Cancer Research
Center, USA
CDD– a database of conserved protein domains created and maintained by the NCBI structure
group
ProDom– a database of comprehensive set of protein domain families automatically generated
from the Swiss-Prot and TrEMBL sequence databases, developed and maintained by the
University Claude Bernard, France
DATABASE
Protein Family Database
Pfam– a database of protein families represented by multiple sequence alignments and hidden
Markov models, constructed and maintained by the Sanger Institute, UK

Protein Function Databases

IMGT– the international immunogenetics information system, a high-quality integrated
knowledge resource of the immune system of human and othervertebrate species, created and
maintained by the University of Montpellier, France
HPA– a website for the human protein atlas which shows expression and localization of proteins
in a large variety of normal human tissues, cancer cells, and cell lines with the aid of
immunohistochemistry images, developed and maintained by Proteome Resource Center, Sweden
DATABASE
Protein Structure Databases
RSCB– the main repository of macromolecular structures maintained by the Research
Collaboration for Structural Bioinformatics
MMDB– the macromolecular database maintained by NCBI
MSD– the entry point for the EBI macromolecular structure database
MSDLite– the EBI web server providing simple search of protein structures
PDBSUM– the EBI web server which provides overview, schematic diagrams, and interactions of
structure
BMRB– the biological magnetic resonance data bank maintained at University of Wisconsin-
Madison
ModBase– the database of comparative protein structure models developed and maintained at
University of California, San Francisco
DATABASE
Classification of Protein Structure
SCOP– the database of Structure Classification of Proteins developed and maintained by
Cambridge University
CATH– the database of Classification, Architecture, Topology, and Homologous superfamily
developed and maintained by the University College London

Visualization of Protein Structure

JenaLib– the Jena Library of Biological Macromolecules which provides information on
macromolecular structures with an emphasis on visualization and analysis
DATABASE
Classification of Protein Structure
SCOP– the database of Structure Classification of Proteins developed and maintained by
Cambridge University
CATH– the database of Classification, Architecture, Topology, and Homologous superfamily
developed and maintained by the University College London

Visualization of Protein Structure

JenaLib– the Jena Library of Biological Macromolecules which provides information on
macromolecular structures with an emphasis on visualization and analysis
DATABASE
Bioinformatics Tools
ExPASy tools– a comprehensive list of online web-based bioinformatics tools provided by
ExPASy and worldwide
http://cn.expasy.org/tools/
EBI tools– the entry page for the EBI bioinformatics tools
http://www.ebi.ac.uk/Tools/
NCBI tools– the entry page for the NCBI bioinformatics tools
http://www.ncbi.nlm.nih.gov/Tools/
DATABASE
Web-based Bioinformatics Platform
EMBOSS explorer– the web interface for the EMBOSS package, maintained by
Ryan Golhar at the University of Medicine and Dentistry of New Jersey
EMBOSS– the web interface for the EMBOSS package, maintained by the
University of Singapore
SRS Tools– the EBI SRS database query server integrates several analysis
packages such as EMBOSS and HMMER which can be launched directly with
retrieved data from the SRS server or with external data provided by users
DATABASE
Sequences Analysis
Dotplot
Dotlet– the Java-based web server for the comparison of DNA and proteinsequences using the
dot plot approach, maintained by the Swiss Institute of Bioinformatics
Pairwise Sequences Alignment
Align– the web server for the pairwise sequence alignment, maintained by EBI. Either global
(Needle) or local (Water) alignment can be performed
BLAST 2– the web server for the alignment of two sequences using BLAST maintained at NCBI.
DATABASE
Multiple Sequences Alignment
ClustalW– the web server for the global multiple sequence alignment program maintained at
EBI. It uses a new version of ClustalW 2.0
Muscle– the web server for the multiple sequence comparison by log-expectation, maintained at
EBI. It claimed to achieve better accuracy with higher speed than ClustalW depending on the
chosen options
MAFAT– the web server of high speed multiple sequence alignment using fast Fourier
transformation, maintained at EBI
KALIGN– the web server of fast and accurate multiple sequence alignment, maintained at EBI
DATABASE
Multiple Sequences Alignment
T- C o ff e e– the web server of several tools for computing, evaluating, and manipulating
multiple alignments of DNA and protein sequences and structures, developed and maintained by
Cedric Notredame at the Center for GenomicRegulation, Spain
DIALIGN– the web server for the multiple sequence alignment, developed and maintained by
Burkhard Morgenstern at Bielefeld University, Germany. It uses alocal alignment approach to
compare a whole segment of sequences without gap penalty
DATABASE
Motif Finding
SMART– the web server for motif discovery and search
http://smart.embl-heidelberg.de/
MEME– the web server for motif discovery and search, developed and main-tained by the
University of California at San Diego
TMHMM– the web server for the prediction of transmembrane helices in proteins, developed and
maintained by Denmark Technical University.
RNA Secondary Structure Prediction
MFOLD– the web server for the prediction of RNA secondary structure, developed and
maintained by Michael Zuker at Rensselaer Polytechnic Institute.
DATABASE SEARCH
BLAST SEARCH
NCBI BLAST– the central point of the NCBI BLAST server which provides whole functionality of
DNA and protein sequence database search programs including PSI-BLAST and PHI-BLAST and
the whole list of databases indifferent scales and different genomes
EBI BLAST– the entry page of the EBI BLAST facility which provides both NCBI BLAST and WU-
BLAST programs as well as a set of specialized BLAST programs to search the alternative
splicing database, the cloning vector database, and the parasite database
WU-BLAST– the entry page of the WU-BLAST maintained by Warren Gishat Washington
University. It provides several links to other BLAST servers worldwide
Sanger BLAST– the entry page of the sequence projects BLAST search services at the Sanger
Institute, featured with the special genome databases generated bythe completed or ongoing
sequencing projects
DATABASE SEARCH
OTHER DATABASE SEARCH
FASTA– the original website for the FASTA set programs maintained by William Pearson at the
University of Virginia. It provides extensive documents and help materials as well
EBI FASTA– the entry page of EBI FASTA services. FASTA has a higher sensitivity in some cases
comparing with BLAST with a slightly lower speed. It is specific to identify low similarity long
regions for highly diverged sequences
MPSrch– the EBI MPSrch server which uses the Smith-Waterman algorithm to obtain the optimal
sequence alignment results
GoldenPath BLAT– the web server for the genome database search, integrated in the
GoldenPath platform
ENSEMBL BLAT– the web server for the genome database search, integratedin the ENSEMBL
platform
MOLECULAR MODELLING
Visualization and Modelling Tools
Swiss PDB Viewer– a comprehensive molecular visualization and modeling package developed by
Nicolas Guex at GlaxoSmithKline. It provides a graphical interface and a user-friendly control panel
for users to analyze several proteins at the same time. There are lots of useful functions such as
superimposition, mutation, and energy minimization for simple molecular simulations
PyMOL– the home page of the molecular visualization system written in Python. It is a user-sponsored
open-source software maintained by DeLano Scientific LLC
Cn3D– the web page of the molecular visualization program Cn3D developed and distributed by
NCBI. It can be installed on your PC to display the three-dimensional structures obtained from the
NCBI MMDB database
Kinemage– the home page of the protein visualization package Kinemage developed and
maintained at the laboratory of Jane Richardson and David Richardson, Duke University
RasMol– the home page of molecular visualization freeware RasMol, maintained by the University of
Massachusetts, Amherst
MOLECULAR MODELLING
Protein Modelling Web Server
Swiss Model– the home page of the automated comparative protein modeling server, hosted by the
University of Basel and the Swiss Institute of Bioinformatics. Extensive documentation and help materials
are provided
3D Jigsaw– the web server to build three-dimensional models for protein molecules based on homologues
of known structure, developed and maintained by the Cancer Research UK
CASP– the entry page for the international protein structure prediction center, hosted at University of
California at Davies. It provides the means of objective testing of evaluation of different methods in
protein structure prediction
PHYLOGENETIC ANALYSIS
Phylogeny Program
Phylogeny software– the whole list of phylogeny programs collected andclassified in groups by Joe
Felsenstein
Online Phylogeny Servers
WebLab Protocols– the WebLab platform we develop and maintain has
integrated the PHYLIP package. The protocols and macros for both
NeighborJoining and maximum parsimony methods are extremely useful for
biologists to construct phylogeny trees with well-defined data sets
NUS EMBOSS interface– the web interface of the PHYLIP programs integrated
in the EMBOSS package, maintained by the University of Singapore
EBC interface– the web interface of some PHYLIP programs, maintained by
Uppsala University, Sweden.
PHYLOGENETIC ANALYSIS
Phylogeny Program
PHYLIP– the website for the comprehensive package Phylogeny Inference Package (PHYLIP) created and maintained by Joe
Felsenstein at the University of Washington. This package can be downloaded and installed on Linux,Windows, and Mac freely
TREE-PUZZLE– the web page for the phylogeny program which uses the maximum likelihood method to analogize nucleotide
and amino acid sequences as well as other two-state data
PA M L– the website for the Phylogenetic Analysis by Maximum Likelihood package developed and maintained by Ziheng
Yang, at University College, London
MEGA– the website for the Molecular Evolutionary Genetics Analysis package developed and maintained by Masatoshi Nei
and his colleagues. It was originally designed for the Windows platform with a graphics interface and uses thedistance method
to construct phylogenetic trees

Display of Phylogenetic Tree

iTOL– the website of the Interactive Tree of Life for the display and manipulationof phylogenetic trees, developed and
maintained by the European MolecularBiology Laboratory
http://itol.embl.de/
PENGANTAR BIOINFORMATIKA

Thank You
DATABASE
Tugas individu
Lakukan pencarian terhadap no Aksesi NM_031650; sajikan print screen hasil
berdasarkan hasil, lakukan identifikasi dan beri penjelasan (dasar justifikasi):
1. Tipe sekuen (mRNA/ protein/ kromosom ?);
2. Ukuran (bp/residues)?
3. Nama protein dan fungsi?
4. Organisme asal?
5. Tanggal final review?
6. Author -publikasi?
7. Title?
8. Jurnal?
9. Nomor aksesi Primary record?
Dalam database NCBI dikenal istilah RefSeq, jelaskan maksud dan kegunaannya?