A Comparison of Methods for Aligning Genomic Sequences

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A Comparison of Methods for Aligning Genomic
Sequences

• JaNera Mitchom
• Fisk University
• Research Alliance for Minorities
• Oak Ridge National Laboratory
• Dr. Mike Leuze
• http//www.csm.ornl.gov

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Outline

• Introduction
• Purpose of Genomic Sequence Analysis
• Background Information
• Central Dogma of Molecular Biology
• Gene Regulation
• Transcription Factor Binding Sites
• Computational Methods of Aligning Genomic
  Sequences
• CLUSTALW
• DIALIGN
• ORNL Method
• Results
• Acknowledgements

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Introduction

• Genomic Sequence Analysis is used to identify
  genomic regulatory regions
• Genes are regulated by proteins called
  transcription factors
• Transcription factors bind to DNA sites found
  close to the gene- regulatory regions
• Regions can be found by sequence comparison and
  may contain binding sites for proteins

The importance of this research is a better
understanding of the way genes are regulated,
which will aid in the development of treatments
for genetic diseases
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Background Information
Central Dogma of Molecular Biology

• DNA specifies RNA, which specifies proteins
• 
  -Francis Crick

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Gene Regulation

• Each cell has copy of entire genome.
• Every gene not expressed in every cell
• Mechanism in each cell that causes the gene to be
  expressed and inhibits expression of other genes

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Transcription Factor Binding Sites

• A section of DNA that transcription
  factors, proteins that control genes expression,
  bind to in order to help transcription of DNA to
  RNA, usually found in close proximity to the gene.

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Computational Methods of Aligning Genomic
Sequences

• Computational methods have been developed
  to identify genomic regulatory regions by
  sequence comparison. CLUSTALW and DIALIGN are two
  computational methods that were compared to a
  method developed at ORNL to determine which
  method is the best for finding these regions.

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FAS(Fatty Acid Synthase)

• Chicken
• Goose
• Important implications in obesity, diabetes,
  artherosclerosis, and cancer

gt Chicken_FAS GGATCCCGTGGGGAGGTTGAGCTGTGCACTAAATGG
AGGAGGTGAATTCT CACAGCTTTCTATTATGACCAAAATATTAACAAAT
AGTTCATTGATCTAA AAAACAGATGGCAAAGAAGGGTGGCGAGGTGGCA
CCGCGGCTGCTACCGG CTTGTGCAAGGAAAGGAGATCCTATAAGCAATG
ACTCCAGCCGACCACAG AGGAAGGCAGAACTCGCCTCACAGCTCACCCC
GCCCAACCCCCCGCACTG
gt Goose_FAS AGTCACCACACAATCGCTTATCGCCTAGCAACACCTAC
CGGGCACGCCAT TGGCAGGCCGCGCCCCCGCCCAACGCCCCCGCCTGAT
TGGGTGCCGGCCC AGGACTGCGCGTCCAGCCGCGCGCCCCTTCTCTTTG
TGCGCTGCCGGGTG CGCGGCGATCCGTGGCCCGGCGCCCGCCCGGCTTC
AGCGCGCCCTGCCGA GCCACGGTGCCGGCGCAGTAGTAGTCCCAACCAC
AGTGTGCACATCCGCG GGGCGGGGGGAGAGGGACACAGAAAGGGACGCG
GCGCTCGCTGCGATGGG
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CLUSTALW

• Uses progressive method of multiple sequence
  analysis
• Basic Alignment Procedure
• Performs pair-wise alignment of sequences
• Produces phylogenetic tree based on alignment
  scores
• Sequences progressively aligned according to
  branching order in phylogenetic tree

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DIALIGN(Diagonal Alignment)

• Uses iterative method of multiple sequence
  alignment
• Basic Alignment Procedure
• Assembles pair-wise and multiple alignments of
  sequences
• Assigns each possible fragment with weight score
  based on probability of random occurrence
• Incorporates sequences into multiple alignment
  based on weight score

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Two Phase ORNL Method

• Developed within the last year.
• Phase One collection of small subsequences that
  match specified criteria
• Phase Two assembly of pieces from phase-one
  collection into larger patterns

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Results

• Showed an importance of similarity in the regions
  closest to the gene
• ORNL method found similarity in several regions
• CLUSTALW and DIALIGN could not find those
  similarities-possibly due to their method of
  alignment

The discovery of these potential regulatory
regions can make the ORNL method a better method
of genomic sequence analysis compared to CLUSTALW
and DIALIGN.
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Results

• Similar regions found by all three methods
• CLUSTALW
• Chicken_FAS TGGCCGCCGGAGGTGGTGGCTGCTTAAATAGCGGTG
  GGAGCTAGAGGGAGA
• Goose_FAS TGGCCGCCGGAGGTGGCGGCTGCTTAAATAGCGGTG
  GGAGCTAGAGGGAGA
• DIALIGN
• Chicken_FAS GTGGCCGCCGGAGGTGGtG GCTGCTTAAA
  TAGCGGTGGG AGCTAGAGGG AGA
• Goose_FAS GTGGCCGCCGGAGGTGGcG GCTGCTTAAA
  TAGCGGTGGG AGCTAGAGGG AGA
• ORNL Method
• Length 52 Substitutions 1 Score
  67.033 2 C AGAGGGAGATCGAGGGTGGCGATAAATTCGTCGG
  TGGTGGAGGCCGCCGGTG 0 G AGAGGGAGATCGAGGGTGGCGA
  TAAATTCGTCGGCGGTGGAGGCCGCCGGTG

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Results

• Region found by ORNL
• Length 28 Substitutions 2 Score
  30.660 404 C CCTGCGCGTCACGGCCCGGCCGTGGGTT
  483 G CCTGCGCGTCAGGACCCGGCCGTGGGTT
• CLUSTALW match
• Chicken_FAS TTGGGTGCCGGCCCGGCACTGCGCGTCC
• Goose_FAS CCGGTCGCAGAGCGCGGCCTTCCACGGC
• DIALIGN match
• Chicken_FAS TTG GGTGCCG-GC CCGGCACTGC GCGTCC
• Goose_FAS CCG GTCGCAGaGC GCGGCCTTCC ACGGCC

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Accomplishments

• Learned PERL
• Compared DNA sequences of two species using three
  computational methods
• Discussed potential applications of comparison
  results
• Prepared research document

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Acknowledgements

• This research was performed under the Research
  Alliance for Minorities Program administered
  through the Computer Science and Mathematics
  Division, Oak Ridge National Laboratory. This
  program is sponsored by the Mathematical,
  Information and Computational Sciences Division,
  Office of Advanced Scientific Computing Research,
  U.S. Department of Energy. Oak Ridge National
  Laboratory is managed by UT-Battelle, LLC, for
  the U.S. Department of Energy under contract
  DE-AC05-00OR22725.
• This work has been authored by a contractor of
  the U.S. Government under contract
  DE-AC05-00OR22725. Accordingly the U.S.
  Government retains a nonexclusive, royalty-free
  license to publish or reproduce the published
  form of this contribution, or allow others to do
  so, for U.S. Government purposes.

I would like to thank Dr. Mike Leuze Dr.
Andrey Gorin Dr. Glenn Allgood Jason
McKay Cheryl Hamby Debbie McCoy