3. What is Bioinformatics?
Bioinformatics represents a new, growing area of science
that uses computational approaches to answer biological
questions.
•Use computer technologies and statistical methods
•Manage and analyze a huge volume of biological data
4. • originated from biology and informatics
• Informatics means analysis of information
• Bioinformatics is the analysis of biological
information
14. DNA Sequence analysis
Catching Errors
Removing vector sequences
Computing/Verifying a Restriction Map
Designing PCR Primers
Analyzing DNA Composition
Establishing the G+C content of your sequence
Finding internal repeats in your sequence
Identifying genome-specific repeats in your sequence
Finding Protein-Coding Regions
ORFing your DNA sequence
Analyzing your DNA sequence with GeneMark
Finding internal exons in vertebrate genomic sequences
Complete gene parsing for eukaryotic genomes
Assembling Sequence Fragments
Managing large sequencing projects
15. Working with a Single Protein Sequence
Predicting the main physico-chemical properties of a protein
Digesting a protein in a computer
Doing Primary Structure Analysis
Looking for transmembrane segments
Looking for coiled-coil regions
Predicting Post-Translational Modifications in Your protein
Finding Known Domains in Your Protein
Discovering New Domains in Your Proteins
17. Practical Examples
Genome annotation
In the context of genomics, annotation is the process of
marking the genes and other biological features in a DNA
sequence.
Computational evolutionary biology
build complex computational models of populations to predict
the outcome of the system over time track and share
information on an increasingly large number of species and
organisms
Biodiversity
Analysis of gene expression
Analysis of regulation of the cell cycle.
Analysis of protein expression
Prediction of protein structure
drug design
predict function of unknown protein
predict reaction of unknown protein with enzymes
working with unknown protein in research
18. Practical Examples …
High-throughput image analysis
• DNA mapping
• RFLP
• Chromosome walking
• Restriction mapping
• Fingerprinting etc.
Genetic Disease analysis
Analysis of mutations in cancer
Uses of Bioinformatics in agriculture
Application of Remote Sensing and GIS for agriculture
Evolutionary studies
Crop improvement
Insect resistance
Improve nutritional quality
Development of Drought resistance varieties
20. PubMed
Reaserch information retrival and analysis
Online Mendelian Inheritance in Man (OMIM)
Catalog of human genes and genetic disorders, with links to associated
literature references, sequence records, BLAST: and related databases.
maps,
The Basic Local Alignment Search Tool for
Protein Function Analysis comparing gene and protein
Algorithms: blastn, megablast,
Compare your protein sequence to the discontiguous derived) protein psi-
secondary (or megablast ,blastp,
blast, phi-blast,tblastn ,tblastx
Databases that contain information on motifs, signatures and protein
domains
Homology and Similarity Tools
Used to identify similarities between novel query sequences of unknown
structure and function with known database
Make specific primers with Primer-BLAST
21. Structural Analysis
Compare structures with the known structure databases
Sequence Analysis
Evolutionary analysis, identification of mutations, hydropathy regions, CpG
islands and Former Famous tool for similarity searching
compositional biases
FASTA
A database search tool used to compare a nucleotide or peptide sequence
to a sequence database
EMBOSS
Sequence alignment : database searching with sequence patterns, protein
motif identification and domain analysis, nucleotide sequence pattern
analysis, codon usage analysis for small genomes, and much more.
22. Clustalw
It produces biologically meaningful multiple sequence alignments , calculates
the best match for the selected sequences, and lines them up so that the
identities, similarities and differences can be seen.
RasMol
Display the structure of DNA, proteins, and smaller molecules. Protein
Explorer, a derivative of RasMol, is an easier to use program.
CDTree
Classify protein sequences and investigating their evolutionary relationships
ProSplign
Utility for computing alignment of proteins to genomic nucleotide sequence.
Specifically accounts for introns and splice signals.
Splign
A utility for computing cDNA-to-Genomic sequence alignments.
23. BLAST Link (BLink)
A link option on protein records that displays the results of a pre-computed
BLAST search of that protein against all other protein sequences .
Huge Capability to working with DNA database
Open Mass Spectrometry Search Algorithm Local Database, Restriction
Include : Making (OMSSA) Search
Efficient search engine for identifyingPrimer Design & spectra by searching
Mapping, MS/MS peptide Analysis, Homology
libraries of known protein sequences. SNP Searching, Protein structure
Searching,
prediction from DNA, Mutation detection
Genome Workbench
An integrated application for viewing and analyzing sequence data.
VecScreen
System for quickly identifying segments of a nucleic acid sequence that may
be of vector origin.
Digital Differential Display (DDD)
A tool for comparing EST profiles in order to identify genes with significantly
different expression levels.
24. Electronic PCR (e-PCR)
e-PCR looks for potential STSs in DNA sequences by searching for
subsequences that closely match the PCR primers and have the correct
order, orientation, and spacing that could represent the PCR primers used
to generate known STSs.
Cn3D
A stand-alone application for viewing 3-dimensional structures from NCBI
PSSM Viewer
Allows users to display, sort, subset and download position-specific score
matrices (PSSMs) either from CDD records or from (PSI)-BLAST
Vector Alignment Search Tool (VAST)
A computer algorithm that identifies similar protein 3-dimensional structures.
Conserved Domain Search Service (CD Search)
Identifies the conserved domains present in a protein sequence.
25. Database of Genotypes and Phenotypes (dbGaP)
Archives and distributes the results of studies that have investigated the
interaction of genotypes and phenotypes.
Genetic Codes
Displays the genetic codes for organisms in the Taxonomy database in
tables and on a taxonomic tree.
Concise Microbial Protein BLAST
A specialized BLAST service in which the queried database consists of all
proteins from complete microbial (prokaryotic) genomes.
Genome ProtMap
Maps each protein from a COG, or in the case of viruses a VOG, back to its
genome, and displays all the genomic segments coding for members of this
particular group of related proteins.
26. Online Mendelian Inheritance in Animals (OMIA)
PubChem Structure Search
PubChem Structure Search allows the PubChem Compound Database to be
queried by chemical structure or chemical structure pattern.
SNP Database Specialized Search Tools
A variety of tools are available for searching the SNP database, allowing
search by genotype, method, population, submitter, markers and sequence
similarity using BLAST.
Viral Genotyping Tool
This tool helps identify the genotype of a viral sequence.
BioAssay Services
Taxonomy Common Tree
Generates a taxonomic tree for a selected group of organisms
28. Table : Genome sequence databases.
Database Description URL
An annotated collection of all publicly
GenBank available nucleotide and protein http://www.ncbi.nlm.ni h.gov
sequences
Curated protein sequence database
SWISS-PROT with a high level of annotation http://www.expasy.org /sport
Genomes online database – a listing
of completed and ongoing genome
GOLD http://www.genomeson line.org
projects Kyoto encyclopedia of
genes
and genomes – integrated suite of http://www.genome.ad .jp/kegg
KEGG databases on genes, proteins, and
metabolic pathways
Integrated database for the analysis
BIOSILICO of metabolism and compound http://biosilico.kaist.ac. kr
structures
29. Table : The existing research on bioinformatics that has applied machine learn-ing techniques.
Research Area Application Reference
http://www.ncbi.nlm.nih.gov/BL AST/
Sequence alignment BLAST, FASTA
http://www.ebi.ac.uk/fasta33/
ClustalWMultAlin http://www.ebi.ac.uk/clustalw/
Multiple sequence alignment DiAlign http://prodes.toulouse.inra.fr/mult alin
http://www.genomatix.de/cgi-bin/dialign/dialign.pl
Genscan http://genes.mit.edu/GENSCAN.h tml
Gene finding GenomeScanGene http://genes.mit.edu/genomescan/
Mark http://www.ebi.ac.uk/genemark/
http://www.sanger.ac.uk/Software /Pfam/
Protein domain analy-sis and Pfam http://www.blocks.fhcrc.org/
identification BLOCKSProDom http://prodes.toulouse.inra.fr/prod om/current/html
Gibbs Sampler http://bayesweb.wadsworth.org/gi bbs/gibbs.html
Pattern identification AlignACE http://atlas.med.harvard.edu/cgi-bin/alignace.pl
MEME http://meme.sdsc.edu/meme/webs ite/intro.html
http://www.embl-heidelberg.de/predictprotein/ pre-
PredictProtein dictprotein.html
Protein folding predic-tion
SwissModle http://www.expasy.org/swissmod
31. Professional softwares
Geneious : Local and web(NCBI) based
CLC DNA Workbench : Local & web based DNA analysis
CLC protien Workbench : Local & web based DNA analysis
Serial Cloner : Advance Primer Design
Mega Blast : Homoly
Gene pellete : Own/ Local Gene Library Builder
Total lab : Protien structure analyzer
32. Freeware
MB analysis : DNA analysis
Anthe Prot : Protein-structure analysis
Blast viewer : Blast result analysis (NCBI tool)
Cn3D : Protein-structure analysis (web based)
SNPphos : SNP search from web
Primer3 : Primer design (NCBI based)
Oligo analysis : Primer analyzer
Bandleader : Gel image analysis
Hyphy 2 : Phylogenetic Tree
36. Unknown gene
Homology Searching
Prediction of mRNA
Prediction of Protein
Unknown Protein
Homology Searching
Prediction of Structure
Prediction of Function
Predicted Functional Protein
Drug Design New Invention New Variety
43. Life Sciences: Applied Science:
Scientific Curator, Gene Analyst, Protein Structural analyst, Molecular Modeler,
Analyst, Phylogenitist, Research Scientist Bio-statistician, Bio-mechanics, Database
/ Associate. programmer.
Computer Science / Pharmaceutial Science:
Engineering: Cheminformatician, Pharmacogenetician,
Pharmacogenomics Research Scientist /
Data base programmer, Bio-informatics Associate.
software developer, Computational
biologist, Network Administrator /
Analyst.
44.
45. • Accelrys • Key Genomics
• Berkeley Lab • Laboratory for Personalized Medicine (LPM)
• BG Medicine • Lilly Singapore Centre for Drug Discovery
• BioCOS Life Sciences • Nagarajan Lab, Washington University
• Biolog, Inc. • NewLink Genetics
• Center for Clinical Epidemiology and • Roche NimbleGen, Inc.
Biostatistics • Roger Williams University - Biology Department
• Curagen Corporation • SAIC Frederick
• Delft University of Technology • Stratagene
• dictyBase • Synamatix Sdn Bhd
• European Bioinformatics Institute (EMBL-EBI) • The Broad Institute of MIT and Harvard
• Fresno State University • The CME Group Inc
• GE Healthcare • University College Dublin
• Gulfstream Bioinformatics • University of Florida, Bioinformatics Faculty
• Harvard Medical School • University of Pittsburgh Bioinformatics Analysis
• Iconix Biosciences Core
• Invitrogen
• J. Craig Venter Institute
• Karolinska Institutet
46.
47. • Bioinformatics is a new exciting area of science.
• Research and development in this area does not
require huge funding
• it requires is a high speed Internet connectivity with
a few powerful computers and a team of enthusiastic
talented people.
48. Bioinformatics Potential in BD
by AR Shikder, PhD
• Development of a World Class Bioinformatics
Institute in BD with BB scientists: As many
Bangladeshi scientists are well placed in
various prestigious institutions almost all over
the world, we could capitalize this opportunity
and develop a world class bioinformatics
institute in Bangladesh.
49. A Student Survival Guideline
Dept. of Biochemistry & Molecular Biology
University of Dhaka , Dhaka, Bangladesh
50. What to Do ?
Read books
Follow Lectures From Famous University
Practice in computer Lab
Regular Workshop
Group Discussion
51. Introduction to Bioinformatics
Arthur M. Lesk, University of Cambridge
Bioinformatics For Dummies®, 2nd Edition
by Jean-Michel Claverie,PhD and Cedric Notredame,PhD
BIOINFORMATICS
A Practical Guide to the Analysis of Genes and Proteins
Andreas D. Baxevanis, National Human Genome Research Institute
B. F. Francis Ouellette, University of British Columbia, Canada
Bioinformatics : Sequence & Genome Analysis
David W. Mount
Bioinformatics Technologies
Yi-Ping Phoebe Chen (Ed.) , Deakin University, Australia
52. Bioinformatics:
genes, proteins and computers
Christine Orengo ; David Jones ; Janet Thornton - UK
Beginning Perl for Bioinformatics
James Tisdall
Bioinformatics Biocomputing and Perl
Michael Moorhouse, The Netherlands ; Paul Barry, Ireland
Foundations of Systems Biology
edited by Hiroaki Kitano
Bioinformatics
Andrzej Polanski , Department of Computer Sciences
Silesian University of Technology, Poland
Developing Bioinformatics Computer Skills
Cynthia Gibas ; Per Jambeck
53. Follow Lectures From Famous University
Open Google webpage
Find Lecture on “ Introduction to Bioinformatics”
Enjoy The Lectures in pdf OR ppt format
54. Practice in computer Lab
Browse website
Use Bioinformatics tools
Take a look on Web based books
Ask Help from teachers
Try to help each other
55. Regular Workshop
We all are teacher & Learner here
Each of us will take a topic and study with it
After a complete study we will share our knowledge with others
We (who are interested) are already working on it
