title: Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN).
abstract: CONCLUSIONS
  Direct PCR sequencing on genetic material containing allelic mixtures results in sequences containing ambiguous nucleotides. Because codons exhibiting allelic mixtures present evidence of evolutionary pressure, it is important to include this information in the assessment of codon synonymy. We developed a program, 'Synonymous-Nonsynonymous Mutation Rates between Sequences Containing Ambiguous Nucleotides' (Syn-SCAN), that calculates synonymous and non-synonymous substitution rates using a model that includes allelic mixtures.
  
  
  BACKGROUND
  Syn-SCAN is implemented on the web and can be downloaded from http://hivdb.stanford.edu.
authors.affiliation: Division of Infectious Diseases, Stanford University Medical Center, 300 Pasteur Drive, Room S-156, CA 94305, USA.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Gonzales
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Dugan
authors.forename: Robert W
authors.initials: RW
authors.lastname: Shafer
mesh_terms: D000483:Alleles; D003062:Codon / Q000235:genetics; D019295:Computational Biology; D015497:HIV-1 / Q000235:genetics; D008957:Models, Genetic; D009154:Mutation; D012984:Software
chemical_list: D003062:Codon