MUSCLE (PowerPoint download)

					       EUAsiaGrid Master Class
            6 May 2010

Enabling Multiple Sequence
   Comparison by Log-
Expectation (MUSCLE) on
        EUAsiaGrid

   By: Lee Hong Kai and Thomas Tay
   NUHS Molecular Diagnostic Center
           Norovirus
• Main pathogen causing non-bacterial
  outbreaks of gastroenteritis
• Easily transmitted in semi-closed
  communities such as hospitals and long-
  term care facilities
• Extremely infectious and a potentially
  dangerous pathogen when present in
  immunocompromised patients.
          Norovirus
•   Small, round +ssRNA virus of about
    50nm
•   Genome size of about 7.5kb, encoding:
    - major structural protein, VP1
    - minor caspid protein, VP2
•   Genetically and antigenically diverse
•       – genotyping of virus strains to
    determine epidemiology link of infected
    patients in an epidemic outbreak or
    transmission event.
          Purpose
• A need for multiple sequence
  alignment of norovirus from
  genogroup I, II and IV
 ‣ Effective primer probe design
 ‣ Phylogeny analysis (sequence
   editing)
 ‣ SNP analysis
 ‣ Check sequence variability
                    Problem
•   ClustalW takes 9hrs for about 1000
    sequences
•   MUSCLE is much faster by still limited
    by memory
     MUSCLE v3.6 by Robert C. Edgar
     http://www.drive5.com/muscle
     This software is donated to the public domain.Please cite: Edgar, R.C.
     Nucleic Acids Res 32(5), 1792-97.
     noro 6423 seqs, max length 7746, avg length 582
     00:05:08 10 MB(2%) Iter       1 100.00% K-mer dist pass 1
     00:05:10 10 MB(2%) Iter       1 100.00% K-mer dist pass 2
     muscle(1066) malloc: *** mmap(size=16777216) failed (error code=12)
     *** error: can't allocate region
     *** set a breakpoint in malloc_error_break to debug
     *** OUT OF MEMORY ***
     Memory allocated so far 10 MB
Thank You!

				
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posted:12/20/2011
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