Yongqiang Zhang,Mohammed J Zaki
Yongqiang Zhang
Background: A structured motif allows variable length gaps between several components, where each component is a simple motif, which allows either no gaps or only fixed length gaps. The motif can either be represented as ...
Yongqiang Zhang,Mohammed J Zaki
Yongqiang Zhang
Background: Extracting motifs from sequences is a mainstay of bioinformatics. We look at the problem of mining structured motifs, which allow variable length gaps between simple motif components. We propose an efficient a...
Reconstructing protein structure from solvent exposure using tabu search [0.03%]
基于禁忌搜索的溶剂暴露蛋白质结构重建方法研究
Martin Paluszewski,Thomas Hamelryck,Pawel Winter
Martin Paluszewski
Background: A new, promising solvent exposure measure, called half-sphere-exposure (HSE), has recently been proposed. Here, we study the reconstruction of a protein's Calpha trace solely from structure-derived HSE informa...
An enhanced RNA alignment benchmark for sequence alignment programs [0.03%]
改进的RNA序列比对数据作为序列比对程序的评测标准
Andreas Wilm,Indra Mainz,Gerhard Steger
Andreas Wilm
Background: The performance of alignment programs is traditionally tested on sets of protein sequences, of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for t...
Jonas S Almeida,Susana Vinga
Jonas S Almeida
The use of Chaos Game Representation (CGR) or its generalization, Universal Sequence Maps (USM), to describe the distribution of biological sequences has been found objectionable because of the fractal structure of that coordinate system. C...
Pattern statistics on Markov chains and sensitivity to parameter estimation [0.03%]
马尔可夫链上的模式统计及对参数估计的敏感性
Grégory Nuel
Grégory Nuel
Background: In order to compute pattern statistics in computational biology a Markov model is commonly used to take into account the sequence composition. Usually its parameter must be estimated. The aim of this paper is ...
Fast calculation of the quartet distance between trees of arbitrary degrees [0.03%]
任意度数树的四联体距离快速计算法
Chris Christiansen,Thomas Mailund,Christian N S Pedersen et al.
Chris Christiansen et al.
Background: A number of algorithms have been developed for calculating the quartet distance between two evolutionary trees on the same set of species. The quartet distance is the number of quartets - sub-trees induced by ...
Gregory A Grothaus,Adeel Mufti,T M Murali
Gregory A Grothaus
Background: Biclustering has emerged as a powerful algorithmic tool for analyzing measurements of gene expression. A number of different methods have emerged for computing biclusters in gene expression data. Many of these...
A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons [0.03%]
用于预测可选择性拼接外显子的谱系泛化隐马尔科夫模型
Jonathan E Allen,Steven L Salzberg
Jonathan E Allen
Background: An important challenge in eukaryotic gene prediction is accurate identification of alternatively spliced exons. Functional transcripts can go undetected in gene expression studies when alternative splicing onl...
A combinatorial optimization approach for diverse motif finding applications [0.03%]
一种用于多种基序寻找应用的组合优化方法
Elena Zaslavsky,Mona Singh
Elena Zaslavsky
Background: Discovering approximately repeated patterns, or motifs, in biological sequences is an important and widely-studied problem in computational molecular biology. Most frequently, motif finding applications arise ...