Computer applications in the biosciences : CABIOS最新文献_第6页

A Brownian dynamics model for the chromatin fiber. 染色质纤维的布朗动力学模型。

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01 DOI: 10.1093/bioinformatics/13.3.271

L Ehrlich, C Münkel, G Chirico, J Langowski

{"title":"A Brownian dynamics model for the chromatin fiber.","authors":"L Ehrlich, C Münkel, G Chirico, J Langowski","doi":"10.1093/bioinformatics/13.3.271","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.3.271","url":null,"abstract":"Motivation: We describe a Brownian dynamics model for the folding of the chromatin fiber based on the model of Woodcock et al. (Proc Natl Acad Sci USA, 90, 9021-9025, 1993). The model takes into account the elastic properties of the DNA as well as the electrostatic interaction and nucleosomal excluded-volume interaction. The solvent is described as a viscous medium, the electrostatic interactions by a screened Coulomb potential.Results: The hydrodynamic properties and their dependence on the solvent's ionic strength are accurately reproduced by the model for nucleosome di- and tetramers. Ionic strength-dependent changes in mobility can be attributed to partial screening of the electrostatic repulsion between different segments of linker DNA. Formation of fiber-like structures occurs on time scales of several hundred microseconds for a linear configuration of 25 nucleosomes. The model was implemented by creating user-defined data types. Use of this so-called object-oriented paradigm allowed for a high degree of component reuse in simulation, analysis and visualization contexts.Availability: The described software is available on request from the authors. Additional information can be found on the WWW at http:/(/)www.dkfz-heidelberg.de/Macromol/ehrlich /chromatin.htm/.","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 3","pages":"271-9"},"PeriodicalIF":0.0,"publicationDate":"1997-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.3.271","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20129529","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: 24

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Seq-Gen:用于沿着系统发育树的DNA序列进化的蒙特卡罗模拟的应用程序。

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01 DOI: 10.1093/bioinformatics/13.3.235

A Rambaut, N C Grassly

引用次数: 1599

Grouper--creation of marker sets for multiplexed genotyping. 石斑鱼——多重基因分型标记集的创建。

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01

R Fuchs

引用次数: 0

The role of long-range interactions in defining the secondary structure of proteins is overestimated. 远程相互作用在确定蛋白质二级结构中的作用被高估了。

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01 DOI: 10.1093/bioinformatics/13.3.297

A Fiser, Z Dosztányi, I Simon

引用次数: 18

Software tool for gene mapping: gRanch. 基因定位软件工具:格兰奇。

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01

Y Wada, K Inoue, K Ohga, H Yasue

引用次数: 0

A new index to find regions showing an unexpected variability or conservation in sequence alignments. 一个新的索引，以发现区域显示意想不到的变化或保守的序列比对。

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01

J Dopazo

引用次数: 0

Prediction of probable genes by Fourier analysis of genomic sequences. 利用基因组序列的傅立叶分析预测可能基因。

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01 DOI: 10.1093/bioinformatics/13.3.263

S Tiwari, S Ramachandran, A Bhattacharya, S Bhattacharya, R Ramaswamy

{"title":"Prediction of probable genes by Fourier analysis of genomic sequences.","authors":"S Tiwari, S Ramachandran, A Bhattacharya, S Bhattacharya, R Ramaswamy","doi":"10.1093/bioinformatics/13.3.263","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.3.263","url":null,"abstract":"MOTIVATION The major signal in coding regions of genomic sequences is a three-base periodicity. Our aim is to use Fourier techniques to analyse this periodicity, and thereby to develop a tool to recognize coding regions in genomic DNA. RESULT The three-base periodicity in the nucleotide arrangement is evidenced as a sharp peak at frequency f = 1/3 in the Fourier (or power) spectrum. From extensive spectral analysis of DNA sequences of total length over 5.5 million base pairs from a wide variety or organisms (including the human genome), and by separately examining coding and non-coding sequences, we find that the relative-height of the peak at f = 1/3 in the Fourier spectrum is a good discriminator of coding potential. This feature is utilized by us to detect probable coding regions in DNA sequences, by examining the local signal-to-noise ratio of the peak within a sliding window. While the overall accuracy is comparable to that of other techniques currently in use, the measure that is presently proposed is independent of training sets or existing database information, and can thus find general application. AVAILABILITY A computer program GeneScan which locates coding open reading frames and exonic regions in genomic sequences has been developed, and is available on request.","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 3","pages":"263-70"},"PeriodicalIF":0.0,"publicationDate":"1997-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.3.263","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20129528","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: 468

'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins. TransMem:在Excel电子表格中实现的神经网络，用于预测蛋白质的跨膜结构域。

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01 DOI: 10.1093/bioinformatics/13.3.231

P Aloy, J Cedano, B Oliva, F X Avilés, E Querol

{"title":"'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins.","authors":"P Aloy, J Cedano, B Oliva, F X Avilés, E Querol","doi":"10.1093/bioinformatics/13.3.231","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.3.231","url":null,"abstract":"Motivation: Genomic sequences from different organisms, even prokaryotic, have plenty of orphan ORFs, making necessary methods for the prediction of protein structure and function. The prediction of the presence of hydrophobic transmembrane (HTM) stretches is a valuable clue for this.Results: The program. TransMem, based on a neural network and running on personal computers (either Apple Macintosh or PC, using Excel worksheets), for the prediction and distribution of amino acid residues in transmembrane segments of integral membrane proteins is reported. The percentage of residue predictive accuracy obtained for the set of proteins tested is 93%, ranging from 99.9% for the best to 71.7% for the worst prediction. The segment-based accuracy is 93.6%; 63.6% of the protein set match any of the predicted and observed segment locations.Availability: TransMem is available upon request or by anonymous up: IP address: luz.uab.es, directory/pub/ TransMem. It is also placed on the EMBL file server (ftp:/(/)ftp.ebi.ac.uk/pub/software/mac/TransMem ).","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 3","pages":"231-4"},"PeriodicalIF":0.0,"publicationDate":"1997-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.3.231","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20130107","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: 24

Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability. Match-Box_server:多序列比对工具，强调可靠性。

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01 DOI: 10.1093/bioinformatics/13.3.249

E Depiereux, G Baudoux, P Briffeuil, I Reginster, X De Bolle, C Vinals, E Feytmans

{"title":"Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability.","authors":"E Depiereux, G Baudoux, P Briffeuil, I Reginster, X De Bolle, C Vinals, E Feytmans","doi":"10.1093/bioinformatics/13.3.249","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.3.249","url":null,"abstract":"Motivation: The Match-Box software comprises protein sequence alignment tools based on strict statistical thresholds of similarity between protein segments. The method circumvents the gap penalty requirement: gaps being the result of the alignment and not a governing parameter of the procedure. The reliable conserved regions outlined by Match-Box are particularly relevant for homology modelling of protein structures, prediction of essential residues for site-directed mutagenesis and oligonucleotide design for cloning homologous genes by polymerase chain reaction (PCR).Results: The method produces reliable results, as assessed by tests performed on protein families of known structures and of low sequence similarity. A reliability score is computed in relation to a threshold of similarity progressively raised to extend the aligned regions to their maximal length, up to the significance limit of matching segments. The score obtained at each position is printed below the sequences and allows a discriminant reading of each aligned region.Availability: Sequences may be submitted to a Web server at http://www.fundp.ac.be/sciences/biologie/bms/+ ++matchbox_submit.html or sent by e-mail to matchbox/biq.fundp.ac.be (help available by just mailing help).","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 3","pages":"249-56"},"PeriodicalIF":0.0,"publicationDate":"1997-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.3.249","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20129526","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: 60

Object-oriented developmental environment for image-analysis applications: implementation for 2D gel electrophoretogram analysis. 面向对象的图像分析应用开发环境:实现二维凝胶电泳分析。

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01

J Pánek, J Vohradský

{"title":"Object-oriented developmental environment for image-analysis applications: implementation for 2D gel electrophoretogram analysis.","authors":"J Pánek, J Vohradský","doi":"","DOIUrl":"","url":null,"abstract":"Motivation: The principal motivation was to design an environment for the development of image-analysis applications which would allow the integration of independent modules into one frame and make available tools for their build-up, running, management and mutual communication.Results: The system was designed as modular, consisting of the core and work modules. The system core focuses on overall management and provides a library of classes for build-up of the work modules, their user interface and data communication. The work modules carry practical implementation of algorithms and data structures for the solution of a particular problem, and were implemented as dynamic-link libraries. They are mutually independent and run as individual threads, communicating with each other via a unified mechanism. The environment was designed to simplify the development and testing of new algorithms or applications. An example of implementation for the particular problem of the analysis of two-dimensional (2D) gel electrophoretograms is presented. The environment was designed for the Windows NT operating system with the use of Microsoft Foundation Class Library employing the possibilities of C++ programming language.Availability: Available on request from the authors.","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 3","pages":"257-62"},"PeriodicalIF":0.0,"publicationDate":"1997-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20129527","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