Informal presentation on bioinformatics
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Here are some suggestions for open online bioinformatics lectures and courses from famous universities: - MIT OpenCourseWare has free bioinformatics course materials and videos from MIT courses. - edX has massive open online courses (MOOCs) in bioinformatics from universities like Harvard, Berkeley, MIT. Some are free to audit. - Coursera has bioinformatics courses from top universities like Johns Hopkins, University of Toronto, Peking University. - YouTube has full lecture videos from bioinformatics courses at universities like Stanford, UC San Diego, University of Cambridge. - Khan Academy has introductory bioinformatics lectures on topics like sequence alignment, gene finding, protein structure. - EMBL-
Informal presentation on bioinformatics
- 1. Informal Presentation on Munsi Md. Shahiuzzaman Atai Rabby 4th year, FH- 302 4th year, SH-307
- 2. Realm of Introduction Bioinformatics Career in Our Plan Bioinformatics
- 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
- 6. Correlated subjects Biology Biochemistry Molecular Biology Microbiology Genetic engineering Mathematics Statistics Computer science.
- 7. Requirements for Bioinformatics research • Biological background • Computer knowledge • Internet browsing experience • Creativity
- 8. Route to become Bioinformatician Biology Computer C O B M I P O U L T O E G R Y Bioinformatician
- 9. • Computer • Internet connection
- 11. Lab apparatus WebPages Software Computer tools
- 12. • Analyze huge volume of data • Don’t need expensive wet lab • Same research can be repeated many times • No adverse effect • Time saving
- 13. In respect of Biochemistry & Molecular Biology
- 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
- 16. RNA analysis structure prediction function prediction translation discovery
- 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
- 19. Working with biological data
- 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
- 30. Make Your Work Easy
- 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
- 35. To Run With Bioinformatics
- 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
- 38. Step-1: Open BLAST Homepage Click the BLASTn button
- 39. Step-2: Browse BLASTn Server Paste your Sequence Here Choose NCBI from the Choose Database pull- down menu. Click the BLAST! button (and wait)
- 40. Step-3: The BLAST intermediate result page Click Format Button
- 41. Step-3: Here is Your Result Now Analyze it with Your Biochemistry Knowledge Graphical View
- 42. Career in Bioinformatics for different stream students
- 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.
- 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
- 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
- 56. Group Discussion You Know very well What it is