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首页> 外文会议>Pacific Symposium on Biocomputing 2001, Jan 3-7, 2001, Mauna Lani, Hawaii >EXACT ALGORITHMS FOR COMPUTING PAIRWISE ALIGNMENTS AND 3-MEDIANS FROM STRUCTURE-ANNOTATED SEQUENCES
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EXACT ALGORITHMS FOR COMPUTING PAIRWISE ALIGNMENTS AND 3-MEDIANS FROM STRUCTURE-ANNOTATED SEQUENCES

机译：精确算法，用于计算带结构注释的序列的对数对齐和3中值

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摘要

Given the problem of mutation saturation in ancient molecular sequences, there is great interest in inferring phylogenies from higher-order types of molecular data that change more slowly, such as genomic organization and the secondary and tertiary structures of ribosomal RNA and proteins. In this paper, we define edit distances based on two representations of RNA secondary structure, arc annotation and hierarchical string annotation, and give algorithms for computing these distances on pairs of annotated sequences, aligning pairs of annotated sequences, and computing 3-median annotated sequences from triples of annotated sequences. The 3-median algorithms can be used as part of a well-known iterative heuristic for inferring phylogenies. All given algorithms are adapted from algorithms for computing longest common annotated subsequences of pairs of annotated sequences.
机译：考虑到古代分子序列中突变饱和的问题，人们非常感兴趣地从变化较慢的高阶分子数据中推断系统发育，例如基因组组织以及核糖体RNA和蛋白质的二级和三级结构。在本文中，我们基于RNA二级结构的两种表示法（弧注释和分层字符串注释）定义编辑距离，并给出了用于在注释序列对上计算这些距离，对齐注释序列对以及计算3中值注释序列的算法来自带注释序列的三元组。 3中值算法可用作推断系统发育的众所周知的迭代启发式算法的一部分。所有给定算法均从用于计算注释序列对中最长的公共注释子序列的算法改编而来。

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