MULTIPLE ALOGNMENT OF SEQUENCES WITH REPEATED AND SHUFFLED ELEMENTS

本子项目是利用由NIH/NCRR资助的中心赠款提供的资源的众多研究子项目之一。子项目和研究者（PI）可能已经从另一个NIH来源获得了主要资金，因此可以在其他CRISP条目中表示。列出的机构是中心的，不一定是研究者的机构。本文介绍了一种新的生物序列多重比对方法ABA （a - bruijn alignment）。ABA与现有的多种比对方法的主要区别在于，ABA将比对表示为一个有向图，可能包含循环。与传统的对齐矩阵或最近引入的偏序对齐（POA）图相比，这种表示提供了更大的灵活性，因为它允许在对齐序列之间存在更大的进化关系。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We describe ABA (A-Bruijn alignment), a new method for multiple alignment of biological sequences. The major difference between ABA and existing multiple alignment methods is that ABA represents an alignment as a directed graph, possibly containing cycles. This representation provides more flexibility than does a traditional alignment matrix or the recently introduced partial order alignment (POA) graph by allowing a larger class of evolutionary relationships between the aligned sequences.