COMPARISON OF MULTIPLE SEQUENCE ALIGNMENT METHODS PERFORMED ON 16S - - PowerPoint PPT Presentation

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COMPARISON OF MULTIPLE SEQUENCE ALIGNMENT METHODS PERFORMED ON 16S - - PowerPoint PPT Presentation

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COMPARISON OF MULTIPLE SEQUENCE ALIGNMENT METHODS PERFORMED ON 16S RIBOSOMAL RNA REFERENCE ALIGNMENTS FOR BACTERIA, ARCHAEA, AND EUKARYOTA BY DARYL DRAKE PROJECT OUTLINE Given reference alignments and their corresponding unaligned sequence

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SLIDE 1

COMPARISON OF MULTIPLE SEQUENCE ALIGNMENT METHODS

PERFORMED ON 16S RIBOSOMAL RNA REFERENCE ALIGNMENTS FOR BACTERIA, ARCHAEA, AND EUKARYOTA BY DARYL DRAKE

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SLIDE 2

PROJECT OUTLINE

  • Given reference alignments and their corresponding unaligned sequence set

perform MSA with MAFFT, CLUSTAL Omega, and MUSCLE

  • Compare running times between different MSA methods
  • Compare alignment to reference alignments using FastSP to determine method

accuracy

  • Perform trials on multiple alignment sizes, sequence lengths, and organism of
  • rigin
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SLIDE 3

INPUT DATA

  • Ribosomal RNA is highly conserved and often used in phylogeny experiments5
  • Will be using UT Austin’s databases of rRNA sequences for several different
  • rganisms
  • Will be focusing on 16s rRNA as it has the lowest rate of evolution
  • Will be looking at Archaea, Bacteria, and Eukaryota
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SLIDE 4

DATA ANAYLSIS

  • CLUSTAL, MUSCLE, and MAFFT all output running time information which will

be used in conjunction with the given information about alignment size

  • FastSP

, a java software package, will be used to quickly calculate SP , TC and modeler score as well as 13 other statistics7

  • Hope to use such information to determine optimal alignment approach for

different levels of genetic conservation (5s vs 16s vs 23s) as well as for different class of organism (Archaea vs Bacteria vs Eukaryota)

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SLIDE 5

SOFTWARE VERSIONS

  • Clustal Omega (Version 1.2.4
  • MAFFT Version 7.305
  • MUSCLE Version 3.825
  • FastSP version 1.6.0
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SLIDE 6

REFERENCES

1.

EMBL-EBI. "Multiple Sequence Alignment." Bioinformatics Tools for Multiple Sequence Alignment. N.p., n.d. Web. 08 Apr. 2017. <http://www.ebi.ac.uk/Tools/msa/>.

2.

Katoh, Kazutaka, Kazuharu Misawa, Kei-ichi Kuma, and Takashi Miyata. "MAFFT: A Novel Method for Rapid Multiple Sequence Alignment Based on Fast Fourier Transform." Nucleic Acids Research. Oxford University Press, 15 July 2002. Web. 03 Apr. 2017.

3.

Edgar, R. C. "MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput." Nucleic Acids Research. U.S. National Library

  • f Medicine, 19 Mar. 2004. Web. 08 Apr. 2017. <https://www.ncbi.nlm.nih.gov/pubmed/15034147>.

4.

Sievers, Fabian, Andreas Wilm, David Dineen, Toby J. Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D. Thompson, and Desmond G. Higgins. "Fast, Scalable Generation of High-quality Protein Multiple Sequence Alignments Using Clustal Omega." Molecular Systems Biology. Nature Publishing Group, 2011. Web. 08 Apr. 2017. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261699/>.

5.

Woese, C. R., and G. E. Fox. "Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms." Proceedings of the National Academy

  • f Sciences of the United States of America. U.S. National Library of Medicine, Nov. 1977. Web. 11 Apr. 2017.

<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC432104/>.

6.

"Comparative RNA Web Site and Project The Gutell Lab." Sequence Alignment Retrieval. N.p., n.d. Web. 11 Apr. 2017. <http://www.rna.ccbb.utexas.edu/DAT/3C/Alignment/>.

7.

Mirarab, S., and T. Warnow. "FASTSP: Linear Time Calculation of Alignment Accuracy." Bioinformatics 27.23 (2011): 3250-258. Web.