on Bioinformatics - University of North Carolina at Chapel Hill

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2 Οκτ 2013 (πριν από 3 χρόνια και 9 μήνες)

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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?

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 sequence

Protein structure

Protein 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

GTTTATGATT

70%

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 Project



Gene array technology



Comparative genomics



Functional 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

http://bioinformatics.weizmann.ac.il/cards/

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