Bioinformatics Training

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MBC
Bioinformatics
Preecha Leangaramgul Medical Biotechnology Center
(MBC), Department of Medical Sciences, Ministry
of Public Health
Bioinformatics Training
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MBC
Introduction to Bioinformatics

• Overview
• System in MBC GCG Wisconsin Package
• Databases supported in WP
• SeqLab and SeqWeb

Bioinformatics Training
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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

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- 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
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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
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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

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System in MBC
MBC
Bioinformatics Training
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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
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MBC
Total HD 1879 GB Used 492
GB Available 1387 GB Capacity 74
server
storage
server
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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

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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

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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

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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
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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

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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

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Unix Command line
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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

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• 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

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Available Programs in SeqLab
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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

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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

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Thank you
Bioinformatics Training