Introduction to Bioinformatics

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Introduction to Bioinformatics. Dr. Rybarczyk, PhD University of North Carolina-Chapel Hill brybar@med.unc.edu. What is Bioinformatics?. What is Bioinformatics?. - PowerPoint PPT Presentation

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Introduction toBioinformatics

Dr. Rybarczyk, PhDUniversity of North Carolina-Chapel Hill

brybar@med.unc.edu

What is Bioinformatics?

What is Bioinformatics?

Conceptualizing biology in terms of molecules and then applying “informatics” techniques from math,

computer science, and statistics to understand and organize the information associated with these

molecules on a large scale

Objectives:

• Identify appropriate search tools for your needs

• Perform searches using ‘unknown’ sequence data

• Analyze protein structure using Protein Explorer

Why do we use Bioinformatics?

• Store/retrieve biological information (databases)

• Retrieve/compare gene sequences

• Predict function of unknown genes/proteins

• Search for previously known functions of a gene

• Compare data with other researchers

• Compile/distribute data for other researchers

Central Dogma

DNA

RNA

Protein

Genomic sequence

RNA function & structure

Protein sequenceProtein structureProtein Function

Phenotype

Computer Tools Used in Bioinformatics

NCBI

GenBank

Internet resources

Sequence retrieval:

Sequence comparison programs:

Protein Structure:

BLAST

modeling prediction programs – RasMol, Protein Explorer

GCG MacVector

Similarity Searching:

A tool for searching gene or protein sequence databases for related genes of interest

The structure, function, and evolution of a gene may be determined by such comparisons

Alignments between the query sequence and any given database sequence, allowing for mismatches and gaps, indicate their degree of similarity

Algorithms

Finds best matching pair comparisons of sequences

input output

Computer comparisons using mathematical probabilities

MRCKTETGAR

MRCGTETGAR

% similarity

90%

CATTATGATA

GTTTATGATT70%

Sequence Analysis:

Determine correct sequence of DNA

Compare sequence with known sequences

Translate DNA into protein sequence

Understand protein function in context

Current Tools Used in Bioinformatics

Strengths:

Accessibility

Growing rapidly

User friendly

Weaknesses:

Sometimes not up-to-date

Limited possibilities

Limited comparisons and information

Not accurate

Need for improved Bioinformatics

Genomics: Human Genome ProjectGene array technologyComparative genomicsFunctional genomics

Proteomics:

Global view of protein function

Protein motifs

Structural databases

Data Mining

Handling enormous amounts of data

Sort through what is important and what is not

Manipulate and analyze data to find patterns and variations that correlate with biological function

3-D Protein Modeling

• Uses information determined by crystal structure methods

• Visualization of protein structure

• Make protein-protein comparisons

• Used to determine:

conformation/folding

antibody binding sites

protein-protein interaction sites

computer aided drug design

Summary

• Introduction to Bioinformatics tools:

Genbank, BLAST, GCG, GeneCard, Chime

• How Bioinformatics is used

• Advantages and disadvantages of tools

• Applications

bioinformatics

students educators

researchers institutions

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