DNA SEQUENCING AND COMPARISON

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DNA SEQUENCING AND COMPARISON

• CS 731
• Professor Heng Ji
• Presented by Keith Hockaday

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INTRODUCTION

• THERE ARE TWO TYPES OF CELLS
• Prokaryotic
• single celled organism
• Eukaryotic
• multi-cellular organism
• My Presentation will focus on the eukaryotic cell

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DNA/RNA

• They are nucleic acids found in the nucleus
• of a cell
• They have double helix structure

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GENE EXPRESSION

• The sequence of A, C, T, and Gs are converted
  into a
• sequence of amino acids
• Isolating a gene from a DNA molecule
• Transcription (mRNA)
• Translation (3D structure protein)

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EXTRACTING DNA

• http//learn.genetics.utah.edu/content/labs/extrac
  tion/
• The process will yield chromosomes

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GENOME

• What is a genome
• The human genome project and BIOINFORMATICS

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COMPARING DNA SEQUENCES
Represents one of the hardest problems that a
computer can solve NP Hard exponential The
Algorithm LCS problem Two
sequences 10 characters long
require 1,048,576 comparisons To see animation
of the comparisons http//69.123.166.15782/DNA_S
EQUENCER.php
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WEB TOOLS

• 1) PROTOGENE
• Web Server http//www.tcoffee.o
  rg/
• It accepts a protein sequence
  and returns the
• associated nucleotide
  sequence.

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WEB TOOLS

• 2) NCBI (National center for Biotechnology
  information)
• http//www.ncbi.nlm.nih.g
  ov/
• software and tools are
  downloadable
• 3) BLASTP (Basic Local Assignment Search
  Tool-Protein)
• A web tool hosted by NCBI
  

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A SIMPLE EXAMPLE

• Search NCBI for insulin protein sequence
• I received this hit
• mapwmhlltvallalwgpnsvqayssqhlcgsnlvealymtcgrsgf
  yr phdrreledqveqaelgleagglqpsalemilqkrgivdqccnnict
  fn qlqnycnvp
• Enter the sequence in PROTOGENE
• The results are listed below in the text
  area.

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AN EXAMPLE USING BLASTP

• BLASTP can be accessed at this location
• http//blast.ncbi.nlm.n
  ih.gov/Blast.cgi

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(No Transcript)
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RESULTS

• Each line corresponds to a bar on the previous
  slide

LOCUS P12497 1435 aa linear VRL 14-OCT-2008
DEFINITION ACCESSION P12497 VERSION
P12497.3 GI77416886 DBSOURCE swissprot locus
POL_HV1N5, accession P12497 created Oct 1,
1989. sequence
updated Jan 23, 2007. ORGANISM Human
immunodeficiency virus type 1 (NEW YORK-5
ISOLATE)
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Perl Application

• Main.pl is program that automates the entire
• procedure.
• My plan is to convert the Perl Application
• into in architecture consisting of
• PHP
• MySql
• Apache
• To be hosted at
• http//69.123.166.15782/DNA_SEQUENCER.php