Clustal W and Clustal X version 2.0

SUMMARY: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. AVAILABILITY: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/     

基于香菇菌株rDNA-ITS序列的系统发育分析

根据真菌核糖体通用引物ITS1和ITS4扩增出13个福建袋栽香菇主要菌株的5.8S rDNA、ITS序列,对该序列进行测序后,得到完整的5.8S rDNA、ITS序列,将该序列提交NCBI并获得登录号,对该序列进行比对分析并构建了系统发育树,从分子水平对香菇菌株进行了区分鉴定,结果显示13个菌株可以明显的分成2丛,而其他菌株又可以从一丛中延伸出几个亚丛。     

CASA: a server for the critical assessment of protein sequence alignment accuracy

SUMMARY: A public server for evaluating the accuracy of protein sequence alignment methods is presented. CASA is an implementation of the alignment accuracy benchmark presented by Sauder et al. (Proteins, 40, 6-22, 2000). The benchmark currently contains 39321 pairwise protein structure alignments produced with the CE program from SCOP domain definitions. The server produces graphical and tabular comparisons of the accuracy of a user's input sequence alignments with other commonly used programs, such as BLAST, PSI-BLAST, Clustal W, and SAM-T99. AVAILABILITY: The server is located at http://capb.dbi.udel.edu/casa.     

Applying MSSIM combined chaos game representation to genome sequences analysis

Converting DNA sequence to image by using chaos game representation (CGR) is an effective genome sequence pretreatment technology, which provides the basis for further analysis between the different genes. In this paper, we have constructed 10 mammal species, 48 hepatitis E virus (HEV), and 10 kinds of bacteria genetic CGR images, respectively, to calculate the mean structural similarity (MSSIM) coefficient between every two CGR images. From our analysis, the MSSIM coefficient of gene CGR images can accurately reflect the similarity degrees between different genomes. Hierarchical clustering analysis was used to calculate the class affiliation and construct a dendrogram. Large numbers of experiments showed that this method gives comparable results to the traditional Clustal X phylogenetic tree construction method, and is significantly faster in the clustering analysis process. Meanwhile MSSIM combined CGR method was also able to efficiently clustering of large genome sequences, which the traditional multiple sequence alignment methods (e.g. Clustal X, Clustal Omega, Clustal W, et al.) cannot classify.     

Clustal W—蛋白质与核酸序列分析软件

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。     

Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome

Background  

Computer programs for the generation of multiple sequence alignments such as "Clustal W" allow detection of regions that are most conserved among many sequence variants. However, even for regions that are equally conserved, their potential utility as hybridization targets varies. Mismatches in sequence variants are more disruptive in some duplexes than in others. Additionally, the propensity for self-interactions amongst oligonucleotides targeting conserved regions differs and the structure of target regions themselves can also influence hybridization efficiency. There is a need to develop software that will employ thermodynamic selection criteria for finding optimal hybridization targets in related sequences.     

Fast,scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

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.     

Comparison of two alignment techniques within a single complex data set: POY versus Clustal

Sensitivity analyses can be performed with respect to different methodologies, differential analytical parameters or models within a single methodology, or alignment parameters. The latter investigations are particularly relevant when divergence and/or the size of molecular data sets make alignment of sequences difficult. Sensitivity analyses are often performed for analyses incorporating Direct Optimization (via POY), either to select optimal alignment parameters or to investigate the stability of topology across parameter sets. Such investigations are rarely, if ever, performed for Clustal alignments as some manual adjustments are nearly always incorporated in the final alignment. Exploration of the performance of both POY and Clustal for a large insect data set incorporating three genes (18S, 28S, H3) and morphology reveals that the performance of POY, as measured by and ILD metric, is predictable across the landscape topology with minimal incongruence when all parameters are treated equally. In contrast, Clustal alignment followed by parsimony analysis yields a landscape with less overall variance, but less predictable behaviour across the parameter topology. © The Willi Hennig Society 2005.     

Clustalnet: the joining of Clustal and CORBA

MOTIVATION: Performing sequence alignment operations from a different program than the original sequence alignment code, and/or through a network connection, is often required. Interactive alignment editors and large-scale biological data analysis are common examples where such a flexibility is important. Interoperability between the alignment engine and the client should be obtained regardless of the architectures and programming languages of the server and client. RESULTS: Clustalnet, a Clustal alignment CORBA server is described, which was developed on the basis of Clustalw. This server brings the robustness of the algorithms and implementations of Clustal to a new level of reuse. A Clustalnet server object can be accessed from a program, transparently through the network. We present interfaces to perform the alignment operations and to control these operations via immutable contexts. The interfaces that select the contexts do not depend on the nature of the operation to be performed, making the design modular. The IDL interfaces presented here are not specific to Clustal and can be implemented on top of different sequence alignment algorithm implementations.     

CLOURE: Clustal Output Reformatter,a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics

We describe a program (and a website) to reformat the ClustalX/ClustalW outputs to a format that is widely used in the presentation of sequence alignment data in SNP analysis and molecular systematic studies. This program, CLOURE, CLustal OUtput REformatter, takes the multiple sequence alignment file (nucleic acid or protein) generated from Clustal as input files. The CLOURE-D format presents the Clustal alignment in a format that highlights only the different nucleotides/residues relative to the first query sequence. The program has been written in Visual Basic and will run on a Windows platform. The downloadable program, as well as a web-based server which has also been developed, can be accessed at http://imtech.res.in/~anand/cloure.html.     

A simple sensitive program for detecting internal repeats in sets of multiply aligned homologous proteins

We designed a simple but sensitive program, IntraCompare, for identifying internal repeats in families of homologous proteins. The protein sequences are aligned (Clustal X), the regions to be compared are selected, and all potential repeat sequences are compared with all others. The output provides comparison scores (GAP program) expressed in standard deviations.     

4种细菌芽胞中α/β-SASP分子结构对比分析

认识和描述不同细菌芽胞α/β-SASP的分子结构特征,为深入开展以α/β-SASP为靶向修饰的应用技术提供科学依据.运用生物信息学方法和技术,比对分析4种菌株,炭疽芽胞杆菌Ames 株、苏云金芽胞杆菌serovar konkukian 97-27 株、腊样芽胞杆菌ATCC 10987株、枯草芽胞杆菌168 株的α/β-SASP基因及蛋白质一、二、三级结构的异同.基因-ClustalW2;一级结构-ClustalW2和ProtParam tool;二级结构-SOPMA;三级结构-SWISS-MODEL和Swiss-Pdbviewer4.0.1.4种菌株的α/β-SASP基因及蛋白质一、二、三级结构有明显的同源性,炭疽芽胞、苏云金芽胞和腊样芽胞的生物学特征非常相似.在开展细菌芽胞的α/β-SASP基因及生物效应研究时,可以首选苏云金杆菌芽胞或腊样杆菌芽胞作为炭疽杆菌芽胞的试验菌,其次可以选择枯草杆菌芽胞.     

MC64-ClustalWP2: A Highly-Parallel Hybrid Strategy to Align Multiple Sequences in Many-Core Architectures

We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures with many cores. It must be stressed that in such a process, the detailed analysis of both the software and hardware features and peculiarities is of paramount importance to reveal key points to exploit and optimize the full potential of parallelism in many-core CPU systems. The new parallelization approach has focused into the most time-consuming stages of this algorithm. In particular, the so-called progressive alignment has drastically improved the performance, due to a fine-grained approach where the forward and backward loops were unrolled and parallelized. Another key approach has been the implementation of the new algorithm in a hybrid-computing system, integrating both an Intel Xeon multi-core CPU and a Tilera Tile64 many-core card. A comparison with other Clustal W implementations reveals the high-performance of the new algorithm and strategy in many-core CPU architectures, in a scenario where the sequences to align are relatively long (more than 10 kb) and, hence, a many-core GPU hardware cannot be used. Thus, the MC64-ClustalWP2 runs multiple alignments more than 18x than the original Clustal W algorithm, and more than 7x than the best x86 parallel implementation to date, being publicly available through a web service. Besides, these developments have been deployed in cost-effective personal computers and should be useful for life-science researchers, including the identification of identities and differences for mutation/polymorphism analyses, biodiversity and evolutionary studies and for the development of molecular markers for paternity testing, germplasm management and protection, to assist breeding, illegal traffic control, fraud prevention and for the protection of the intellectual property (identification/traceability), including the protected designation of origin, among other applications.     

In vitro and in silico cloning of Xenopus laevis SOD2 cDNA and its phylogenetic analysis

By using the methodology of both wet and dry biology (i.e., RT-PCR and cycle sequencing, and biocomputational technology, respectively) and the data obtained through the Genome Projects, we have cloned Xenopus laevis SOD2 (MnSOD) cDNA and determined its nucleotide sequence. These data and the deduced protein primary structure were compared with all the other SOD2 nucleotide and amino acid sequences from eukaryotes and prokaryotes, published in public databases. The analysis was performed by using both Clustal W, a well known and widely used program for sequence analysis, and AntiClustAl, a new algorithm recently created and implemented by our group. Our results demonstrate a very high conservation of the enzyme amino acid sequence during evolution, which proves a close structure-function relationship. This is to be expected for very ancient molecules endowed with critical biological functions, performed through a specific structural organization. The nucleotide sequence conservation is less pronounced: this too was foreseeable, due to neutral mutations and to the species-specific codon usage. The data obtained by using AntiClustAl are comparable with those produced with Clustal W, which validates this algorithm as an important new tool for biocomputational analysis. Finally, it is noteworthy that evolutionary trees, drawn by using all the available data on SOD2 nucleotide sequences and amino acid and either Clustal W or AntiClustAl, are comparable to those obtained through phylogenetic analysis based on fossil records.     

Structural Characterization of a Unique Peptide in Porin: An Approach Towards Specific Detection of Salmonella enterica Serovar Typhi

International Journal of Peptide Research and Therapeutics - Salmonella OmpC sequence analysis by Clustal revealed a unique amino acid residue (TSNGSNPST) in positions from 268 to 276. This region...     

Incorporation of gap characters and lineage-specific regions into phylogenetic analyses of gene families from divergent clades: an example from the kinesin superfamily across eukaryotes

The kinesin superfamily across eukaryotes was used to examine how incorporation of gap characters scored from conserved regions shared by all members of a gene family and incorporation of amino acid and gap characters scored from lineage‐specific regions affect gene‐tree inference of the gene family as a whole. We addressed these two questions in the context of two different densities of sequence sampling, four alignment programs, and two methods of tree construction. Taken together, our findings suggest the following. First, gap characters should be incorporated into gene‐tree inference, even for divergent sequences. Second, gene regions that are not conserved among all or most sequences sampled should not be automatically discarded without evaluation of potential phylogenetic signal that may be contained in gap and/or sequence characters. Third, among the four alignment programs evaluated using their default alignment parameters, Clustal may be expected to output alignments that result in the greatest gene‐tree resolution and support. Yet, this high resolution and support should be regarded as optimistic, rather than conservative, estimates. Fourth, this same conclusion regarding resolution and support holds for Bayesian gene‐tree analyses relative to parsimony‐jackknife gene‐tree analyses. We suggest that a more conservative approach, such as aligning the sequences using DIALIGN‐T or MAFFT, analyzing the appropriate characters using parsimony, and assessing branch support using the jackknife, is more appropriate for inferring gene trees of divergent gene families. © The Willi Hennig Society 2007.     

扩张蛋白家族蛋白序列分析

以黄瓜CsEXP10蛋白为基础,利用FASTA软件获得了同源性较高的12种扩张蛋白基因序列,同时利用BLOCK软件、ClustalW软件和Tree View软件对13种扩张蛋白进行序列和进化分析。结果显示,扩张蛋白家族有6个保守域,进化上高度保守：这对今岳扩张蛋白的结构构建和功能分析具有指导意义。