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Munsi Md. Shahiuzzaman4th year, FH- 302
Informal Presentation on
Introduction to Bioinformatics
Atai Rabby4th year, SH-307
Introduction
Realm of Bioinformatics
Career in Bioinformatics
Our Plan
Presentation on Introduction to 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
What is Bioinformatics?
• originated from biology and informatics• Informatics means analysis of information• Bioinformatics is the analysis of biological
information
BIOINFORMATICS?
Take a Look
Correlated subjects
BiologyBiochemistryMolecular BiologyMicrobiologyGenetic engineeringMathematicsStatisticsComputer science.
Requirements for Bioinformatics research
• Biological background• Computer knowledge• Internet browsing experience• Creativity
Biology Computer
Bioinformatician
COMPUTER
BIOLOGY
Route to become Bioinformatician
Bioinformatics lab (a Dry lab)
• Computer • Internet connection
WebPages
Software
Computer tools
Lab apparatus
Why Bioinformatics?
• Analyze huge volume of data• Don’t need expensive wet lab• Same research can be repeated many times • No adverse effect• Time saving
In respect of Biochemistry & Molecular Biology
What Bioinformatics Do?
Catching ErrorsRemoving vector sequencesComputing/Verifying a Restriction MapDesigning PCR PrimersAnalyzing DNA CompositionEstablishing the G+C content of your sequenceFinding internal repeats in your sequenceIdentifying genome-specific repeats in your sequenceFinding Protein-Coding RegionsORFing your DNA sequenceAnalyzing your DNA sequence with GeneMarkFinding internal exons in vertebrate genomic sequencesComplete gene parsing for eukaryotic genomesAssembling Sequence FragmentsManaging large sequencing projects
DNA Sequence analysis
Predicting the main physico-chemical properties of a proteinDigesting a protein in a computerDoing Primary Structure AnalysisLooking for transmembrane segmentsLooking for coiled-coil regionsPredicting Post-Translational Modifications in Your proteinFinding Known Domains in Your ProteinDiscovering New Domains in Your Proteins
Working with a Single Protein Sequence
RNA analysis
structure predictionfunction predictiontranslationdiscovery
Genome annotationIn 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
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
Practical Examples …
BIOINFORMATICS TOOLS Working with biological data
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, maps, and related databases.
Protein Function Analysis
Compare your protein sequence to the secondary (or derived) protein
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
BLAST:The Basic Local Alignment Search Tool for comparing gene and protein Algorithms: blastn, megablast, discontiguous megablast ,blastp, psi-blast, phi-blast,tblastn ,tblastx
BIOINFORMATICS TOOLS
Structural Analysis Compare structures with the known structure databases
Sequence Analysis Evolutionary analysis, identification of mutations, hydropathy regions, CpG islands and 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.
BIOINFORMATICS TOOLS
Former Famous tool for similarity searching
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.
BIOINFORMATICS TOOLS
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 .
Open Mass Spectrometry Search Algorithm (OMSSA) Search Efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences.
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.
BIOINFORMATICS TOOLS
Huge Capability to working with DNA database Include : Making Local Database, Restriction Mapping, Primer Design & Analysis, Homology Searching, SNP Searching, Protein structure prediction from DNA, Mutation detection
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.
BIOINFORMATICS TOOLS
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.
BIOINFORMATICS TOOLS
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
BIOINFORMATICS TOOLS
Web Based Resources & Tools
Walking through Internet
Table : Genome sequence databases.
Database Description URL
GenBank An annotated collection of all publicly
available nucleotide and protein sequences
http://www.ncbi.nlm.ni h.gov
SWISS-PROT
Curated protein sequence database with a high level of annotation http://www.expasy.org /sport
GOLD Genomes online database – a listing of
completed and ongoing genome projects Kyoto encyclopedia of genes
http://www.genomeson line.org
KEGG
and genomes – integrated suite of databases on genes, proteins, and
metabolic pathways
http://www.genome.ad .jp/kegg
BIOSILICO Integrated database for the analysis of metabolism and compound structures http://biosilico.kaist.ac. kr
Web Based Resources & Tools
Table : The existing research on bioinformatics that has applied machine learn-ing techniques.
Research Area Application Reference
Sequence alignment BLAST, FASTAhttp://www.ncbi.nlm.nih.gov/BL AST/ http://www.ebi.ac.uk/fasta33/
Multiple sequence alignment
ClustalWMultAlin DiAlign
http://www.ebi.ac.uk/clustalw/ http://prodes.toulouse.inra.fr/mult alinhttp://www.genomatix.de/cgi-bin/dialign/dialign.pl
Gene finding Genscan GenomeScanGeneMark
http://genes.mit.edu/GENSCAN.h tml http://genes.mit.edu/genomescan/ http://www.ebi.ac.uk/genemark/
Protein domain analy-sis and identification
Pfam BLOCKSProDom
http://www.sanger.ac.uk/Software /Pfam/ http://www.blocks.fhcrc.org/ http://prodes.toulouse.inra.fr/prod om/current/html
Pattern identification Gibbs Sampler AlignACE MEME
http://bayesweb.wadsworth.org/gi bbs/gibbs.html http://atlas.med.harvard.edu/cgi-bin/alignace.pl http://meme.sdsc.edu/meme/webs ite/intro.html
Protein folding predic-tion PredictProtein SwissModle
http://www.embl-heidelberg.de/predictprotein/ pre-dictprotein.html http://www.expasy.org/swissmod
Web Based Resources & Tools
Make Your Work Easy
Software for Bioinformatician
Some Professional software & Freeware
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
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
Some Professional software & Freeware
Some Result Page Of Software
To Run With Bioinformatics
Some Says It Is Hard
A Procedure To Invent A New Protein With A New Gene
Unknown gene
Unknown Protein
Predicted Functional Protein
Homology SearchingPrediction of mRNAPrediction of Protein
Homology SearchingPrediction of StructurePrediction of Function
Drug Design New Invention New Variety
Try an ExampleBLASTn
A Procedure of Homology Searching : BLASTn
Step-1: Open BLAST Homepage
Click the BLASTn button
Step-2: Browse BLASTn Server
Paste your Sequence Here
Choose NCBI from the Choose Database pull-
down menu.
Click the BLAST! button (and wait)
A Procedure of Homology Searching : BLASTn
Step-3: The BLAST intermediate result page
Click Format Button
A Procedure of Homology Searching : BLASTn
Step-3: Here is Your Result Now Analyze it with Your Biochemistry Knowledge
A Procedure of Homology Searching : BLASTn
Graphical View
Career in Bioinformatics
for different stream students
Job field in Bioinformatics
Life Sciences: Scientific Curator, Gene Analyst, Protein Analyst, Phylogenitist, Research Scientist / Associate.
Computer Science / Engineering: Data base programmer, Bio-informatics software developer, Computational biologist, Network Administrator / Analyst.
Applied Science: Structural analyst, Molecular Modeler, Bio-statistician, Bio-mechanics, Database programmer.
Pharmaceutial Science: Cheminformatician, Pharmacogenetician, Pharmacogenomics Research Scientist / Associate.
Career opportunity for Bioinformatician
BIOINFORMATICS COMPANIES• Accelrys • Berkeley Lab • BG Medicine • BioCOS Life Sciences • Biolog, Inc. • Center for Clinical Epidemiology and Biostatistics • Curagen Corporation • Delft University of Technology • dictyBase • European Bioinformatics Institute (EMBL-EBI) • Fresno State University • GE Healthcare • Gulfstream Bioinformatics • Harvard Medical School • Iconix Biosciences • Invitrogen • J. Craig Venter Institute
• Karolinska Institutet • Key Genomics • Laboratory for Personalized Medicine (LPM) • Lilly Singapore Centre for Drug Discovery • Nagarajan Lab, Washington University• NewLink Genetics • Roche NimbleGen, Inc. • Roger Williams University - Biology Department • SAIC Frederick • Stratagene • Synamatix Sdn Bhd • The Broad Institute of MIT and Harvard • The CME Group Inc • University College Dublin • University of Florida, Bioinformatics Faculty • University of Pittsburgh Bioinformatics Analysis
Core
Bioinformatics in Bangladesh
• 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.
Bioinformatics in Bangladesh
Bioinformatics Potential in BDby 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.
Our PlanA Student Survival Guideline
Dept. of Biochemistry & Molecular BiologyUniversity of Dhaka , Dhaka, Bangladesh
What to Do ?
Read booksFollow Lectures From Famous UniversityPractice in computer LabRegular WorkshopGroup Discussion
books
Introduction to BioinformaticsArthur M. Lesk, University of Cambridge
Bioinformatics For Dummies®, 2nd Editionby Jean-Michel Claverie,PhD and Cedric Notredame,PhD
BIOINFORMATICSA 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 AnalysisDavid W. Mount
Bioinformatics TechnologiesYi-Ping Phoebe Chen (Ed.) , Deakin University, Australia
Bioinformatics:genes, proteins and computers
Christine Orengo ; David Jones ; Janet Thornton - UK
Beginning Perl for BioinformaticsJames Tisdall
Bioinformatics Biocomputing and PerlMichael Moorhouse, The Netherlands ; Paul Barry, Ireland
Foundations of Systems Biologyedited by Hiroaki Kitano
BioinformaticsAndrzej Polanski , Department of Computer Sciences
Silesian University of Technology, Poland
Developing Bioinformatics Computer SkillsCynthia Gibas ; Per Jambeck
books
Follow Lectures From Famous University
Open Google webpageFind Lecture on “ Introduction to Bioinformatics”Enjoy The Lectures in pdf OR ppt format
Practice in computer Lab
Browse websiteUse Bioinformatics toolsTake a look on Web based books Ask Help from teachersTry to help each other
Regular Workshop
We all are teacher & Learner hereEach 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
Group Discussion
You Know very well What it is
Presented By a.IDEA.master
Thanks . . .
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