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Báo cáo y học: "Phylogenetic assessment of alignments reveals neglected tree signal in gaps"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Phylogenetic assessment of alignments reveals neglected tree signal in gaps. | Dessimoz and Gil Genome Biology 2010 11 R37 http genomebiology.eom content 11 4 R37 w Genome Biology RESEARCH _ Open Access Phylogenetic assessment of alignments reveals neglected tree signal in gaps Christophe Dessimoz 2 and Manuel Gib 1 2 Abstract Background The alignment of biological sequences is of chief importance to most evolutionary and comparative genomics studies yet the two main approaches used to assess alignment accuracy have flaws reference alignments are derived from the biased sample of proteins with known structure and simulated data lack realism. Results Here we introduce tree-based tests of alignment accuracy which not only use large and representative samples of real biological data but also enable the evaluation of the effect of gap placement on phylogenetic inference. We show that i the current belief that consistency-based alignments outperform scoring matrix-based alignments is misguided ii gaps carry substantial phylogenetic signal but are poorly exploited by most alignment and tree building programs iii even so excluding gaps and variable regions is detrimental iv disagreement among alignment programs says little about the accuracy of resulting trees. Conclusions This study provides the broad community relying on sequence alignment with important practical recommendations sets superior standards for assessing alignment accuracy and paves the way for the development of phylogenetic inference methods of significantly higher resolution. Background The study of biological sequences almost inevitably begins with the process of alignment. The goal of this process is usually to match homologous characters that is characters that have a common ancestry 1 . In turn these sets of homologs the columns of the alignment can be used for a variety of applications such as identifying residues with analogous structural or functional role or inferring the phylogenetic tree of the underlying sequences. The accuracy of multiple sequence alignment programs has