Structural Homology in Ribosomal RNA, and a Deliberation on POY
msra(2006)
摘要
>Abstract Computer alignments have been said to be more objective and repeatable than manual alignments. Here we suggest,that computer alignment methods, particularly those using a program called POY, suffer from a series of practical problems, and philosophical inconsistencies.Subjective decisions are still a part of POY analyses, but are less transparent. Wepoint out the problems POY has with ancestral state reconstruction under conditions of nucleotide compositional bias, its problems when gaps are not uniformly distributed, and its problems when gaps are not independent of one-another. In ribosomal RNA (rRNA), the individual nucleotides are less important than the structure within which they are associated. This higher level of conservation dictates that structures should be aligned before nucleotides. Weshow,with an empirical example that manual alignments can be more repeatable, more objective, and more accurate than POY analyses, and call into question the conclusions drawn from POY analyses of rRNA data. >Key,words
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关键词
poy,rrna,> key words alignment,sensitivity analyses.,secondary structure
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