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Bioinformatics Training

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1. Softwares - Unix command line - SeqLab : X-Window user interface ... GCG Wisconsin Package Softwares. Bioinformatics Training. MBC. System in MBC ... – PowerPoint PPT presentation

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Title: Bioinformatics Training


1
MBC
Bioinformatics
Preecha Leangaramgul Medical Biotechnology Center
(MBC), Department of Medical Sciences, Ministry
of Public Health
Bioinformatics Training
2
MBC
Introduction to Bioinformatics
  • Overview
  • System in MBC GCG Wisconsin Package
  • Databases supported in WP
  • SeqLab and SeqWeb

Bioinformatics Training
3
MBC
What is Bioinformatics?
  • Application of computer technology to
    management of biological information
  • Computer are used gather, store, analyze and
    integrate biological and
  • genetic information such as nucleotide and
    amino acid sequences
  • Information can be applied to gene-based drug
    discovery and development
  • Biology, Computer Science, Mathematics and
    Information Technology merge to
  • form a single discipline

Bioinformatics Training
4
MBC
- The development and implementation of tools
that enable efficient access to, and use and
management of, various types of information -
The development of new algorithms (mathematical
formulas) and statistics with which to
assess relationships among members of large data
sets, such as methods to locate a gene
within a sequence, predict protein structure
and/or function, and cluster protein
sequences into families of related sequences
Bioinformatics Training
5
MBC
Bioinformatics System in MBC
GCG Wisconsin Package (Accelrys) 1.
Softwares - Unix command line - SeqLab
X-Window user interface - SeqWeb Web-based
graphical user interface Internet Explorer
2. Databases - Nucleic Acid - Protein
Bioinformatics Training
6
MBC
GCG Wisconsin Package Softwares
  • A complete suit of over 130 programs designed
    for all aspects of biological
  • sequence analysis
  • Modular each program performs a specific
    function to achieve different
  • goals but can be combined in different ways to
    address various analytical
  • problems
  • Flexible can add other Accelrys bioinformatics
    products, in-house to
  • extend its functionality
  • Customizable each program has a unique set of
    options to change its
  • behavior and output

Bioinformatics Training
7
System in MBC
MBC
Bioinformatics Training
8
System Setup Server SUN Fire280R
Server 2 GB RAM, 80 GB HD OS Version Solaris
9 Host name MBC01 Storage SUN Storage
A1000 and SUN Storage 3320 /data with 266 GB on
A1000 /data2 with 739 GB on 3320 /data3 with
739 GB on 3320 /data4 with 135 GB on A1000
MBC
Bioinformatics Training
9
MBC
Total HD 1879 GB Used 492
GB Available 1387 GB Capacity 74
server
storage
server
Bioinformatics Training
10
MBC
Databases supported in the Wisconsin Package
  • GCG formatted sequence databases
  • 2 nucleic acid and 5 protein databases updated
    regularly
  • Usage of these databases greatly enhances the
    functionalities of the programs,
  • increases the search speed

Bioinformatics Training
11
MBC
Databases Nucleic Acid
  • GCG combined GenBank and EMBL to form
    GenEMBLPlus containing
  • all of GenBank and an abridged EMBL for data
    that are not present
  • in GenBank
  • Databases are released bi-monthly following
    GenBanks release schedule
  • GCG formatted databases follow the GenBank
    organization

Bioinformatics Training
12
MBC
Nucleotide Database Divisions
  • EMBLPlus (abridged) emp
  • GenBankPlus gbp
  • GenEMBLPlus gep
  • Expressed Sequence Tags (EST)
  • - est gb_est em_est
  • Genome Survey Sequences (GSS)
  • - gss gb_gss em_gss
  • High-Throughput cDNA Sequences (HTC)
  • - htc gb_htc

Bioinformatics Training
13
MBC
Databases Protein
The Wisconsin Package contains the following
public protein database - PIR Protein
Information Resource from the National Biomedical
Research Foundation (NBRF) -
SWISS-PROT Swiss Protein Database by Dr. Amos
Bairoch at the Swiss Institute of
Bioinformatics (SIB) - SP-TrEMBL
Translated EMBL database in SWISS-PROT format.
A joint effort by Dr. Bairoch and the
European Bioinformatics Institute
(EBI) - GenPept Translated GenBank
Database, no annotation - NRL_3D a
structural database produced by PIR from
sequence information extracted from 3-D
structures in PDB
Bioinformatics Training
14
MBC
Databases Protein
  • PIR pir
  • - PIR1 pir1
  • - PIR2 pir2
  • - PIR3 pir3
  • - PIR4 pir4
  • SWISS-PROT sw
  • SP-TrEMBL sptr
  • SWISS-PROTPlus Combination of SWISS-PROT and
    SP-TrEMBL
  • - swp
  • GenPept gp
  • NRL_3D nrl_3d

Bioinformatics Training
15
MBC
GCG Wisconsin Package with SeqLab Interface
  • Installed and run under UNIX
  • - More disk space for database and
    results
  • - Run on CPUs for computer intensive
    analysis
  • - Multi-user access and easy maintenance
  • Native interface for the Wisconsin Package (WP)
    UNIX command line
  • Graphical user interface (GUI) for WP on UNIX
    an X-Window interface

Bioinformatics Training
16
MBC
Unix Command line
Bioinformatics Training
17
MBC
Available Programs in SeqLab
  • Comparison
  • compare two or more sequences
  • Database Searching
  • use the sequences to search peptide and nucleic
    acid databases
  • Evolution
  • investigate the evolutionary relationships
    within a group of sequences
  • Mapping
  • display restriction maps or peptide cleavage
    maps of the sequence
  • Gene Finding and Pattern Recognition
  • recognize coding regions, terminators, repeats,
    and consensus patterns

Bioinformatics Training
18
MBC
  • Primer Selection
  • select oligonucleotide primers for a template
    DNA sequence
  • Protein Analysis
  • perform protein analysis tasks such as find
    structural and sequence motifs,
  • find transmembrane regions, find
    helix-turn-helix motifs
  • Nucleic Acid Secondary Structure
  • predict secondary structure in nucleic acid
    sequences
  • Translation
  • translate nucleic acids into peptide sequences
    and peptides back into
  • nucleic acids

Bioinformatics Training
19
MBC
Available Programs in SeqLab
Bioinformatics Training
20
MBC
Bioinformatics Training
21
MBC
GCG Wisconsin Package with SeqWeb Interface
  • A Web-based graphical user interface to access
    the WP in intranet
  • Provides parameter control and extensive on-line
    help about the algorithms,
  • parameters and results
  • Produces results with links to both internal and
    external data
  • Offers multi-program analyses as one-step
    operations
  • Allows users to save results as text, graphics
    or HTML documents

Bioinformatics Training
22
MBC
Available Programs in SeqWeb
  • Access the most frequently used programs in the
    Wisconsin Package
  • - Database searching and retrieval
  • - Sequence comparison
  • - Protein analysis
  • - Mapping
  • - Evolutionary analysis
  • - Pattern recognition and motif searching
  • - Nucleic acid secondary structure
  • - Primer prediction

Bioinformatics Training
23
MBC
Bioinformatics Training
24
MBC
Bioinformatics Training
25
MBC
Thank you
Bioinformatics Training
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