منابع مشابه
Near-Optimal Block Alignments
In this paper, we improve the idea of the near-optimal alignments. Though the near optimal alignments increase the possibility to find the correct alignment, too many of them may confuse the biologists. So we present the filter scheme for the near-optimal alignments. An easy method to trace the nearoptimal alignments and an algorithm to filter those alignments are proposed.1 The time complexity...
متن کاملVisualization of near-optimal sequence alignments
MOTIVATION Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near-optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for finding effectively the most biologically meaningful a...
متن کاملBetter Tree Alignments through Near-optimal Intermediates 1
The reconstruction of hypothetical ancestral sequences is a widely used means to guide algorithms for multiple alignment and phylogeny reconstruction on the basis of an evolutionary tree. We identify the common framework to which many of these algorithms conform, and provide two essential improvements, unifying cases with and without given alignment. Particularly, our techniques enable the use ...
متن کاملApplying Near-Optimal Alignments to Protein Structure Prediction
The prediction of three-dimensional protein structures from onedimensional amino acid sequence information is an important and interesting problem, as much can be learned about a protein’s function from the way that it is folded. There are many different ways to approach this problem, but they all tend to fall into three basic categories: homology modeling, fold recognition, and ab initio predi...
متن کاملOptimal alignments in linear space
Space, not time, is often the limiting factor when computing optimal sequence alignments, and a number of recent papers in the biology literature have proposed space-saving strategies. However, a 1975 computer science paper by Hirschberg presented a method that is superior to the new proposals, both in theory and in practice. The goal of this paper is to give Hirschberg's idea the visibility it...
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ژورنال
عنوان ژورنال: IEICE Transactions on Information and Systems
سال: 2008
ISSN: 0916-8532,1745-1361
DOI: 10.1093/ietisy/e91-d.3.789