Computer applications in the biosciences : CABIOS最新文献

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A genetic algorithm for multiple molecular sequence alignment. 多分子序列比对的遗传算法。
Computer applications in the biosciences : CABIOS Pub Date : 1997-12-01 DOI: 10.1093/bioinformatics/13.6.565
C Zhang, A K Wong
{"title":"A genetic algorithm for multiple molecular sequence alignment.","authors":"C Zhang,&nbsp;A K Wong","doi":"10.1093/bioinformatics/13.6.565","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.6.565","url":null,"abstract":"<p><strong>Motivation: </strong>Multiple molecular sequence alignment is among the most important and most challenging tasks in computational biology. The currently used alignment techniques are characterized by great computational complexity, which prevents their wider use. This research is aimed at developing a new technique for efficient multiple sequence alignment.</p><p><strong>Approach: </strong>The new method is based on genetic algorithms. Genetic algorithms are stochastic approaches for efficient and robust searching. By converting biomolecular sequence alignment into a problem of searching for optimal or near-optimal points in an 'alignment space', a genetic algorithm can be used to find good alignments very efficiently.</p><p><strong>Results: </strong>Experiments on real data sets have shown that the average computing time of this technique may be two or three orders lower than that of a technique based on pairwise dynamic programming, while the alignment qualities are very similar.</p><p><strong>Availability: </strong>A C program on UNIX has been written to implement the technique. It is available on request from the authors.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.6.565","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20401802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 110
XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences. XDOM是一种图形化工具,用于分析任何一组蛋白质序列中的结构域排列。
Computer applications in the biosciences : CABIOS Pub Date : 1997-12-01 DOI: 10.1093/bioinformatics/13.6.601
J Gouzy, P Eugéne, E A Greene, D Kahn, F Corpet
{"title":"XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences.","authors":"J Gouzy,&nbsp;P Eugéne,&nbsp;E A Greene,&nbsp;D Kahn,&nbsp;F Corpet","doi":"10.1093/bioinformatics/13.6.601","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.6.601","url":null,"abstract":"<p><strong>Motivation: </strong>To extract the maximum possible information from a set of protein sequences, its modular organization must be known and clearly displayed. This is important both for structural and functional analysis.</p><p><strong>Results: </strong>This paper presents an algorithm and a graphical interface called XDOM which performs a systematic analysis of the modular organization of any set of protein sequences. The algorithm is an automatic method to identify putative domains from sequence comparisons. The graphical tool displays the proteins as a set of linked boxes, corresponding to its domains. The method has been tested on a family of bacterial proteins and on whole genomes. It is currently applied to the complete SWISS-PROT database to build the PRODOM database.</p><p><strong>Availability: </strong>XDOM is available free of charge by anonymous ftp:¿¿ftp://ftp.toulouse.inra.fr/pub/xdom¿ ¿. The ProDom database can be consulted at ¿¿http://protein.toulouse.inra.fr/prodom.html¿¿.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.6.601","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20401806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 30
DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. DCA:一种有效的分而治之的方法来同时多序列比对。
Computer applications in the biosciences : CABIOS Pub Date : 1997-12-01 DOI: 10.1093/bioinformatics/13.6.625
J Stoye, V Moulton, A W Dress
{"title":"DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment.","authors":"J Stoye,&nbsp;V Moulton,&nbsp;A W Dress","doi":"10.1093/bioinformatics/13.6.625","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.6.625","url":null,"abstract":"<p><strong>Motivation: </strong>DCA is a new computer program for multiple sequence alignment which utilizes a 'divide-and-conquer' type of heuristic approach.</p><p><strong>Availability: </strong>The algorithm is freely available from http://bibiserv.TechFak.Uni-Bielefeld.DE/dca/.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.6.625","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20401812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 115
Displaying the information contents of structural RNA alignments: the structure logos. 显示结构RNA比对的信息内容:结构标识。
Computer applications in the biosciences : CABIOS Pub Date : 1997-12-01 DOI: 10.1093/bioinformatics/13.6.583
J Gorodkin, L J Heyer, S Brunak, G D Stormo
{"title":"Displaying the information contents of structural RNA alignments: the structure logos.","authors":"J Gorodkin,&nbsp;L J Heyer,&nbsp;S Brunak,&nbsp;G D Stormo","doi":"10.1093/bioinformatics/13.6.583","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.6.583","url":null,"abstract":"<p><strong>Motivation: </strong>We extend the standard 'Sequence Logo' method of Schneider and Stevens (Nucleic Acids Res., 18, 6097-6100, 1990) to incorporate prior frequencies on the bases, allow for gaps in the alignments, and indicate the mutual information of base-paired regions in RNA.</p><p><strong>Results: </strong>Given an alignment of RNA sequences with the base pairings indicated, the program will calculate the information at each position, including the mutual information of the base pairs, and display the results in a 'Structure Logo'. Alignments without base pairing can also be displayed in a 'Sequence Logo', but still allowing gaps and incorporating prior frequencies if desired.</p><p><strong>Availability: </strong>The code is available from, and an Internet server can be used to run the program at, http://www.cbs.dtu.dk/gorodkin/appl/slogo. html.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.6.583","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20401803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 183
BioWish: a molecular biology command extension to Tcl/Tk. 一个分子生物学命令扩展到Tcl/Tk。
T Sicheritz-Pontén
{"title":"BioWish: a molecular biology command extension to Tcl/Tk.","authors":"T Sicheritz-Pontén","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20401810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Two applications to facilitate the viewing of database search result files on the Macintosh. 两个应用程序,方便在Macintosh上查看数据库搜索结果文件。
Computer applications in the biosciences : CABIOS Pub Date : 1997-12-01 DOI: 10.1093/bioinformatics/13.6.623
A S Law, D W Burt
{"title":"Two applications to facilitate the viewing of database search result files on the Macintosh.","authors":"A S Law,&nbsp;D W Burt","doi":"10.1093/bioinformatics/13.6.623","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.6.623","url":null,"abstract":"<p><strong>Motivation: </strong>MacBOB (Macintosh BLAST Output Browser) and MacBOB Filter are two Macintosh-based applications that greatly simplify the viewing of BLAST and FASTA search results files.</p><p><strong>Availability: </strong>The programs can be obtained via anonymous ftp from ftp.ri.bbsrc.ac.uk from the directory/pub/software/MacBOB, or via WWW from the Roslin Institute Home Page (http://www.ri.bbsrc.ac.uk/).</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.6.623","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20401811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
BioWish: a molecular biology command extension to Tcl/Tk 一个分子生物学命令扩展到Tcl/Tk
Computer applications in the biosciences : CABIOS Pub Date : 1997-12-01 DOI: 10.1093/bioinformatics/13.6.621
Thomas Sicheritz-Pontén
{"title":"BioWish: a molecular biology command extension to Tcl/Tk","authors":"Thomas Sicheritz-Pontén","doi":"10.1093/bioinformatics/13.6.621","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.6.621","url":null,"abstract":"The Tcl/Tk (Ousterhout, 1994) scripting language has proved to be a powerful tool for building programs involved in the analysis of molecular sequence data. However, typical 'biological' operations, like the translation of a nucleotide sequence to the corresponding amino acid sequence, or the calculation of the G + C content in different codon positions in a 50 kbp cosmid sequence, are performed far too slowly with the standard Tel commands. To circumvent this problem, we have constructed a library that extends the Tcl/Tk language by adding primitive operators suited for sequence analysis implemented in the C-language. Additional commands related to molecular biology, written in Tel, are included. Built as a shared library, usage is easy and does not require modification of the Tcl/Tk source code. BioWish can be obtained from the WWW site http://evolution.bmc.uu.se/~thomas/moLlinux. The distribution consists of a single C-source file which should compile without modifications on all Unix systems capable of dynamical loading. It requires Tel 7.5/Tk4.1 or higher. No patching of the Tcl/Tk core is required. On systems where dynamic loading is not available, BioWish can be compiled as a standalone Tk intepreter.","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.6.621","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60766779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
The Sequence Alerting Server--a new WEB server. 序列警报服务器——一个新的WEB服务器。
Computer applications in the biosciences : CABIOS Pub Date : 1997-12-01 DOI: 10.1093/bioinformatics/13.6.619
H Hegyi, J M Lai, P Bork
{"title":"The Sequence Alerting Server--a new WEB server.","authors":"H Hegyi,&nbsp;J M Lai,&nbsp;P Bork","doi":"10.1093/bioinformatics/13.6.619","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.6.619","url":null,"abstract":"<p><strong>Unlabelled: </strong>A Sequence Alerting Server with a WWW interface is described which informs users with query sequences in database searches about new entries in protein databases related to their query.</p><p><strong>Availability: </strong>The server address is http://www.bork.embl-heidelberg.de/alerting/.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.6.619","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20401809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements. SS3D-P2:基于二级结构元素的蛋白质基序的三维亚结构搜索程序。
Computer applications in the biosciences : CABIOS Pub Date : 1997-12-01 DOI: 10.1093/bioinformatics/13.6.593
H Kato, Y Takahashi
{"title":"SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements.","authors":"H Kato,&nbsp;Y Takahashi","doi":"10.1093/bioinformatics/13.6.593","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.6.593","url":null,"abstract":"<p><p>This paper discusses the implementation of a three-dimensional (3D) structure motif search of proteins. Each protein structure is represented by a set of secondary structure elements (SSEs) which involves alpha-helix segments and beta-strand segments. In describing it, every SSE is further reduced into a two-node graph that consists of the starting amino acid residue, the ending residue and a pseudo-bond between them. The searching algorithm is based on a graph theoretical clique-finding algorithm that has been used for 3D substructure searching in small organic molecules. The program SS3D-P2 was validated using proteins that have well-known 3D motifs, and it correctly found the Greek key motif within an eye lens protein, crystallin, that consists of four anti-parallel beta strands. The program was also successfully applied to searching for the more complex 3D motif, TIM-type beta-barrel motif, with a protein structure database from the Protein Data Bank.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.6.593","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20401805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
SAMBA: hardware accelerator for biological sequence comparison. SAMBA:用于生物序列比较的硬件加速器。
Computer applications in the biosciences : CABIOS Pub Date : 1997-12-01 DOI: 10.1093/bioinformatics/13.6.609
P Guerdoux-Jamet, D Lavenier
{"title":"SAMBA: hardware accelerator for biological sequence comparison.","authors":"P Guerdoux-Jamet,&nbsp;D Lavenier","doi":"10.1093/bioinformatics/13.6.609","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.6.609","url":null,"abstract":"MOTIVATION SAMBA (Systolic Accelerator for Molecular Biological Applications) is a 128 processor hardware accelerator for speeding up the sequence comparison process. The short-term objective is to provide a low-cost board to boost PC or workstation performance on this class of applications. This paper places SAMBA amongst other existing systems and highlights the original features. RESULTS Real performance obtained from the prototype is demonstrated. For example, a sequence of 300 amino acids is scanned against SWISS-PROT-34 (21 210 389 residues) in 30 s using the Smith and Waterman algorithm. More time-consuming applications, like the bank-to-bank comparison, are computed in a few hours instead of days on standard workstations. Technology allows the prototype to fit onto a single PCI board for plugging into any PC or workstation. AVAILABILITY SAMBA can be tested on the WEB server at URL http://www.irisa.fr/SAMBA/.","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1997-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.6.609","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20401807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 75
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