Informal presentation on bioinformatics

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.


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.


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.


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.


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.


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


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


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


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)


Step-3: The BLAST intermediate result page

Click Format Button


Step-3: Here is Your Result Now Analyze it with Your Biochemistry Knowledge


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 . . .

Documents

Informal presentation on bioinformatics