共查询到19条相似文献,搜索用时 78 毫秒
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多序列比对能够揭示出一系列DNA或蛋白质序列之间的关系,发现序列间的保守区域主要介绍了几种较为常用的多序列比对程序及其使用技巧. 相似文献
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为了解决生物信息学中基因多序列比对的计算速度慢和软件陈旧的问题,提出了基于Yarn(Yet Another Resource Negotiator)云平台的生物基因多序列比对并行计算方法Yarn_clustalW。分析了clustalW算法的数学模型及其面向MapReduce的任务划分方式,Yarn_clustalW中综合考虑了基因的长度和数目,采用一种基于阈值刻度的任务划分方式。利用NCBI的GenBank生物基因数据作为案例程序进行了测试。实验结果表明:Yarn_clustalW比起多序列比对clustalW串行计算方法具有更快的运行时间与加速比,可以使生物科研人员节省很多时间与精力,方便对于药物靶标的发现,缩短生物药物的开发周期。 相似文献
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Clustal W—蛋白质与核酸序列分析软件 总被引:2,自引:1,他引:2
蛋白质与核酸的序列分析在现代生物学和生物信息学中发挥着重要作用,新的算法和软件层出不穷,本文介绍一个可运行在PC机上的完全免费的多序列比较软件-ClustalW,它不但可以进行蛋白质与核酸的多序列比较,分析不同序列之间的相似性关系,还可以绘制进化树。由于其灵活的输入输出格式、方便的参数设定和选择、详尽的在线帮助以及良好的可移植性,使得ClustalW在蛋白质与核酸的序列分析中得到了广泛应用。 相似文献
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David Dineen Toby J Gibson Kevin Karplus Weizhong Li Rodrigo Lopez Hamish McWilliam Michael Remmert Johannes Söding Julie D Thompson Desmond G Higgins 《Molecular systems biology》2011,7(1)
Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high‐quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high‐quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam. 相似文献
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Protein multiple sequence alignment is an important bioinformatics tool. It has important applications in biological evolution analysis and protein structure prediction. A variety of alignment algorithms in this field have achieved great success. However, each algorithm has its own inherent deficiencies. In this paper, permutation similarity is proposed to evaluate several protein multiple sequence alignment algorithms that are widely used currently. As the permutation similarity method only concerns the relative order of different protein evolutionary distances, without taking into account the slight difference between the evolutionary distances, it can get more robust evaluations. The longest common subsequence method is adopted to define the similarity between different permutations. Using these methods, we assessed Dialign, Tcoffee, ClustalW and Muscle and made comparisons among them. 相似文献
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The many faces of sequence alignment 总被引:9,自引:0,他引:9
Batzoglou S 《Briefings in bioinformatics》2005,6(1):6-22
Starting with the sequencing of the mouse genome in 2002, we have entered a period where the main focus of genomics will be to compare multiple genomes in order to learn about human biology and evolution at the DNA level. Alignment methods are the main computational component of this endeavour. This short review aims to summarise the current status of research in alignments, emphasising large-scale genomic comparisons and suggesting possible directions that will be explored in the near future. 相似文献
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Routinely used multiple-sequence alignment methods use only sequence information. Consequently, they may produce inaccurate alignments. Multiple-structure alignment methods, on the other hand, optimize structural alignment by ignoring sequence information. Here, we present an optimization method that unifies sequence and structure information. The alignment score is based on standard amino acid substitution probabilities combined with newly computed three-dimensional structure alignment probabilities. The advantage of our alignment scheme is in its ability to produce more accurate multiple alignments. We demonstrate the usefulness of the method in three applications: 1) computing more accurate multiple-sequence alignments, 2) analyzing protein conformational changes, and 3) computation of amino acid structure-sequence conservation with application to protein-protein docking prediction. The method is available at http://bioinfo3d.cs.tau.ac.il/staccato/. 相似文献
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SNUFER is a software for the automatic localization and generation of tables used for the presentation of single nucleotide
polymorphisms (SNPs). After input of a fasta file containing the sequences to be analyzed, a multiple sequence alignment is
generated using ClustalW ran inside SNUFER. The ClustalW output file is then used to generate a table which displays the
SNPs detected in the aligned sequences and their degree of similarity. This table can be exported to Microsoft Word,
Microsoft Excel or as a single text file, permitting further editing for publication. The software was written using Delphi
7 for programming and FireBird 2.0 for sequence database management. It is freely available for noncommercial use and can be
downloaded from
http://www.heranza.com.br/bioinformatica2.htm. 相似文献
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Aniba MR Siguenza S Friedrich A Plewniak F Poch O Marchler-Bauer A Thompson JD 《Briefings in bioinformatics》2009,10(1):11-23
The traditional approach to bioinformatics analyses relies onindependent task-specific services and applications, using differentinput and output formats, often idiosyncratic, and frequentlynot designed to inter-operate. In general, such analyses wereperformed by experts who manually verified the results obtainedat each step in the process. Today, the amount of bioinformaticsinformation continuously being produced means that handlingthe various applications used to study this information presentsa major data management and analysis challenge to researchers.It is now impossible to manually analyse all this informationand new approaches are needed that are capable of processingthe large-scale heterogeneous data in order to extract the pertinentinformation. We review the recent use of integrated expert systemsaimed at providing more efficient knowledge extraction for bioinformaticsresearch. A general methodology for building knowledge-basedexpert systems is described, focusing on the unstructured informationmanagement architecture, UIMA, which provides facilities forboth data and process management. A case study involving a multiplealignment expert system prototype called AlexSys is also presented. 相似文献
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A novel method has been developed for acquiring the correct alignment of a query sequence against remotely homologous proteins by extracting structural information from profiles of multiple structure alignment. A systematic search algorithm combined with a group of score functions based on sequence information and structural information has been introduced in this procedure. A limited number of top solutions (15,000) with high scores were selected as candidates for further examination. On a test-set comprising 301 proteins from 75 protein families with sequence identity less than 30%, the proportion of proteins with completely correct alignment as first candidate was improved to 39.8% by our method, whereas the typical performance of existing sequence-based alignment methods was only between 16.1% and 22.7%. Furthermore, multiple candidates for possible alignment were provided in our approach, which dramatically increased the possibility of finding correct alignment, such that completely correct alignments were found amongst the top-ranked 1000 candidates in 88.3% of the proteins. With the assistance of a sequence database, completely correct alignment solutions were achieved amongst the top 1000 candidates in 94.3% of the proteins. From such a limited number of candidates, it would become possible to identify more correct alignment using a more time-consuming but more powerful method with more detailed structural information, such as side-chain packing and energy minimization, etc. The results indicate that the novel alignment strategy could be helpful for extending the application of highly reliable methods for fold identification and homology modeling to a huge number of homologous proteins of low sequence similarity. Details of the methods, together with the results and implications for future development are presented. 相似文献
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Löytynoja A Goldman N 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2008,363(1512):3913-3919
We have developed a phylogeny-aware progressive alignment method that recognizes insertions and deletions as distinct evolutionary events and thus avoids systematic errors created by traditional alignment methods. We now extend this method to simultaneously model regional heterogeneity and evolution. This novel method can be flexibly adapted to alignment of nucleotide or amino acid sequences evolving under processes that vary over genomic regions and, being fully probabilistic, provides an estimate of regional heterogeneity of the evolutionary process along the alignment and a measure of local reliability of the solution. Furthermore, the evolutionary modelling of substitution process permits adjusting the sensitivity and specificity of the alignment and, if high specificity is aimed at, leaving sequences unaligned when their divergence is beyond a meaningful detection of homology. 相似文献