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

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 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 origin

INPUT DATA • Ribosomal RNA is highly conserved and often used in phylogeny experiments 5 • Will be using UT Austin’s databases of rRNA sequences for several different organisms • Will be focusing on 16s rRNA as it has the lowest rate of evolution • Will be looking at Archaea, Bacteria, and Eukaryota

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 statistics 7 • 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)

SOFTWARE VERSIONS • Clustal Omega (Version 1.2.4 • MAFFT Version 7.305 • MUSCLE Version 3.825 • FastSP version 1.6.0

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 of 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 of 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.