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Dr. Mohammad Najafi Iran University of Medical Sciences DATA D A T A D A T A D A T A Introductory For Bioinformatics

DATA D A T A D A T A D A T A ِ David Roos: “We are swimming in rapidly rising of data …..how do we help from drowning?”

DATA D A T A D A T A D A T A ”..We must hook our individual computers into the worldwide network that gives us access to daily changes in the databases and also makes immediate our communications with each other……….. The programs that display and analyze the material for us must be improved - and we must learn to use them more effectively. Like the purchased kits, they will make our life easier, but also like the kits, we must understand enough of how they work to use them effectively…” Walter Gilbert (1991) “Towards a paradigm shift in biology” Nature News and Views 349:99

DATA D A T A D A T A D A T A BIOINFORMATICS The field of science is in which Biology,Computer science and Informational technology merge to form a single discipline

DATA D A T A D A T A D A T A Bioinformatics The creation and advancement of algorithms, computational and statistical techniques for management and analysis of biological data. Clinical Bioinformatics The hypothesis driven of a medical subject using computers and carried out with experiment.

To computerize the current knowledge of molecular interactions Metabolic pathways Regulatory pathways Molecular assemblies DATA D A T A D A T A D A T A Biochemical Pathways

DATA D A T A D A T A D A T A Current servers BioCarta KEGG MetaCyc

DATA D A T A D A T A D A T A Sectors and Subsectors

DATA D A T A D A T A D A T A Gene Databases BioCarta KEEG MetaCyc

DATA D A T A D A T A D A T A Protein Database PIR ( P rotein I nformation R esource) PDB ( P rotein D ata B ank) HPRD ( H uman P rotein R eference D atabase)

DATA D A T A D A T A D A T A ALIGNMENT

DATA D A T A D A T A D A T A Similarity between two sequences Global Local

DATA D A T A D A T A D A T A what is the best alignment between the two sequences? How should alignments be scored? How should gaps be scored?

DATA D A T A D A T A D A T A Scoring system for nucleic acids Match = +1 (ex; A-A, T-T, C-C, G-G) Mismatch = -1(ex; A-T, A-C, etc.)

DATA D A T A D A T A D A T A PAM-Point Accepted Mutation [Evolutionary Model] Margaret Dayhoff, 1978 related proteins

DATA D A T A D A T A D A T A BLOSUM-Block Substitutions [Conserved Sequence] Henikoff and Henikoff, 1992 conserved, ungapped regions of a protein family

DATA D A T A D A T A D A T A

D A T A D A T A D A T A

D A T A D A T A D A T A Alignment Tools Pairwise alignment BLAST FASTA Dot Plat Multiple sequence alignment (MSA) Induced pairwise method Progressive method Statistical Value Graph

DATA D A T A D A T A D A T A

D A T A D A T A D A T A Multiple Sequence Alignment

DATA D A T A D A T A D A T A Progressive Method (MSA)

DATA D A T A D A T A D A T A Progressive Method (Tree)

DATA D A T A D A T A D A T A The Fruits of analyses of the sequences that exit within the primary sources Secondary Protein Database

DATA D A T A D A T A D A T A PSProsite BL blocks PD Prodom PR prints IPR Interpro PF pfam Secondary Protein Database

DATA D A T A D A T A D A T A Gene Regulation Databases Related to compilation of DNA Elements & Protein Regulatory Factors Protein Regulatory Factors

DATA D A T A D A T A D A T A Promoter region The element of bind with polymerase II - EPD - EPD The sequence beyond TATA box - TRRD - TRRD -TRANCFAC -TRANCFAC Gene Regulation Databases

DATA D A T A D A T A D A T A Genomics Gene Prediction ab initio Homology Consensus

DATA D A T A D A T A D A T A Proteomics protein expression Mapping protein expression to estimate what’s actually happing in tissue following intervention

DATA D A T A D A T A D A T A Proteome analysis purification 1.A procedure for purification 2-DE 2-DE structural information 2.A method to determine structural information Sequencing Sequencing Ms Ms databases 3.Use of databases genebank genebank functional information 4.Prediction of functional information using annotations using annotations

Najafi M,Jangravi Z. Human PON promoters: from similarity to prediction of polymorphic positions within transcription factor elements. Mini Rev Med Chem Sep;10(10): Najafi M, Roustazadeh A. Scoring of Matrix Gla protein (MGP) promoter variants within predicted transcription elements. IWBBIO 2013, Najafi M, Alipoor B, Shabani M, Amirfarhangi A, Ghasemi H.Association between rs4673 (C/T) and rs (A/G) haplotypes of NAD(P)H oxidase p22phox gene and severity of stenosis in coronary arteries. Gene ;499(1): Najafi M, Roustazadeh A, Alipoor B. Ox-LDL Particles: Modified components, Cellular uptake, Biological roles and Clinical assessments. Cardiovasc Hematol Disord Drug Targets Oct 26. Najafi M, Bioinformatics Tools as Power Hypothetical Predictors. Biochem Physiol :e113. References

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