发布求助
文献互助 智能选刊 最新文献

Computer applications in the biosciences : CABIOS最新文献

筛选
英文 中文
A new dynamic tool to perform assembly of expressed sequence tags (ESTs). 一个新的动态工具来执行表达序列标签(est)的组装。
Computer applications in the biosciences : CABIOS Pub Date : 1997-08-01 DOI: 10.1093/bioinformatics/13.4.453
R W Gill, T C Hodgman, C B Littler, M D Oxer, D S Montgomery, S Taylor, P Sanseau
{"title":"A new dynamic tool to perform assembly of expressed sequence tags (ESTs).","authors":"R W Gill,&nbsp;T C Hodgman,&nbsp;C B Littler,&nbsp;M D Oxer,&nbsp;D S Montgomery,&nbsp;S Taylor,&nbsp;P Sanseau","doi":"10.1093/bioinformatics/13.4.453","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.453","url":null,"abstract":"<p><strong>Motivation: </strong>Expressed Sequence Tags (ESTs) are short single-pass DNA sequences obtained from either ends of cDNA clones. To exploit these sequences efficiently, a dynamic Web-tool has been developed which uses these data to perform fast virtual cloning of cDNAs.</p><p><strong>Results: </strong>Starting with a query sequence, the user is able to identify related ESTs and extend the sequence of interest step by step, possibly to a full-length transcript. Graphical views of the clustering are used to monitor the progress of a particular 'cloning' project. Potential open reading frames are detected by positional base preference, and hyperlinks to other Worldwide Web sites allows the user to retrieve information relevant to each EST in a cluster (e.g. sequence traces, clone size, plate position). Apart from cDNA cloning, this tool also provides a mechanism for collating gene families and polymorphism sites.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"453-7"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.453","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20224210","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: 28
Identifying distantly related protein sequences. 鉴定远亲蛋白序列。
Computer applications in the biosciences : CABIOS Pub Date : 1997-08-01 DOI: 10.1093/bioinformatics/13.4.325
W R Pearson
{"title":"Identifying distantly related protein sequences.","authors":"W R Pearson","doi":"10.1093/bioinformatics/13.4.325","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.325","url":null,"abstract":"","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"325-32"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.325","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20225044","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: 31
Micado--a network-oriented database for microbial genomes. Micado——一个面向网络的微生物基因组数据库。
Computer applications in the biosciences : CABIOS Pub Date : 1997-08-01 DOI: 10.1093/bioinformatics/13.4.431
V Biaudet, F Samson, P Bessières
{"title":"Micado--a network-oriented database for microbial genomes.","authors":"V Biaudet,&nbsp;F Samson,&nbsp;P Bessières","doi":"10.1093/bioinformatics/13.4.431","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.431","url":null,"abstract":"<p><strong>Motivation: </strong>We created Micado, a database for managing genomic information, as part of the Bacillus subtilis genome programs. Its content will be progressively extended to the whole microbial world.</p><p><strong>Results: </strong>A relational schema is defined for selective queries. It links eubacterial and archaeal sequences, genetic maps for Bacillus subtilis and Escherichia coli, and information on mutants. The latter comes from a new functional analysis project of unknown genes in B subtilis, and the database allows the community to curate information. To help queries from users, a graphical interface is built on SQL access to the database and provided through the WWW. We have automated imports of microbial sequences, and E. coli genetic map, by programming parsers of flat file distributions. These ensure smooth updates from molecular biology repositories on the Internet. Hyperlinks are created as a complement, to reference other general and specialized related information resources.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"431-8"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.431","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20225663","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: 36
Calculation of daylength. 计算日长。
Computer applications in the biosciences : CABIOS Pub Date : 1997-08-01 DOI: 10.1093/bioinformatics/13.4.479
J S Amthor
{"title":"Calculation of daylength.","authors":"J S Amthor","doi":"10.1093/bioinformatics/13.4.479","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.479","url":null,"abstract":"where /is is the hour angle of the Sun (angular distance from the meridian of a site in radians) at sunset. Sunrise and sunset are not exactly symmetrical about the time that the Sun reaches a local meridian, but for biological simulation purposes the symmetry implicit in equation (1) is acceptable. The geometric equation for sin a (where a is solar elevation) can be rearranged to find hs as follows:","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"479-80"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.479","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20224215","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
EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. EST_GENOME:一个将剪接的DNA序列与未剪接的基因组DNA对齐的程序。
Computer applications in the biosciences : CABIOS Pub Date : 1997-08-01 DOI: 10.1093/bioinformatics/13.4.477
R Mott
{"title":"EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA.","authors":"R Mott","doi":"10.1093/bioinformatics/13.4.477","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.477","url":null,"abstract":"","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"477-8"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.477","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20224214","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: 293
Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. jannaschi甲烷球菌基因组序列分析及蛋白功能预测。
Computer applications in the biosciences : CABIOS Pub Date : 1997-08-01 DOI: 10.1093/bioinformatics/13.4.481
M Andrade, G Casari, A de Daruvar, C Sander, R Schneider, J Tamames, A Valencia, C Ouzounis
{"title":"Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function.","authors":"M Andrade,&nbsp;G Casari,&nbsp;A de Daruvar,&nbsp;C Sander,&nbsp;R Schneider,&nbsp;J Tamames,&nbsp;A Valencia,&nbsp;C Ouzounis","doi":"10.1093/bioinformatics/13.4.481","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.481","url":null,"abstract":"","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"481-3"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.481","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20224216","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
Sisyphus and prediction of protein structure. 西西弗斯与蛋白质结构预测。
Computer applications in the biosciences : CABIOS Pub Date : 1997-08-01 DOI: 10.1093/bioinformatics/13.4.345
B Rost, S O'Donoghue
{"title":"Sisyphus and prediction of protein structure.","authors":"B Rost,&nbsp;S O'Donoghue","doi":"10.1093/bioinformatics/13.4.345","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.345","url":null,"abstract":"<p><p>The problem of predicting protein structure from the sequence remains fundamentally unsolved despite more than three decades of intensive research effort. However, new and promising methods in three-dimensional (3D), 2D and 1D prediction have reopened the field. Mean-force-potentials derived from the protein databases can distinguish between correct and incorrect models (3D). Inter-residue contacts (2D) can be detected by analysis of correlated mutations, albeit with low accuracy. Secondary structure, solvent accessibility and transmembrane helices (1D) can be predicted with significantly improved accuracy using multiple sequence alignments. Some of these new prediction methods have proven accurate and reliable enough to be useful in genome analysis, and in experimental structure determination. Moreover, the new generation of theoretical methods is increasingly influencing experiments in molecular biology.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"345-56"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.345","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20225046","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: 53
DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis. DnaSP 2.0版:一个新颖的软件包，广泛的分子群体遗传学分析。
Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01
J Rozas, R Rozas
{"title":"DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis.","authors":"J Rozas,&nbsp;R Rozas","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Motivation: </strong>Several methods in molecular population genetics have recently been described to estimate the amount and pattern of the DNA polymorphism in natural populations, and also to test the neutral theory of molecular evolution. These methods are essential for understanding the molecular evolutionary process. However, a comprehensive computer program for the analysis is not currently available.</p><p><strong>Results: </strong>Here we present DnaSP (DNA Sequence Polymorphism) version 2.0, a software package for Windows that performs extensive population genetics analyses on DNA sequence data. DnaSP estimates several measures of DNA sequence variation within and between populations, linkage disequilibrium, recombination, gene flow and gene conversion (a new algorithm to detect gene conversion tracts has been included). DnaSP can also carry out several tests of neutrality: those of Fu and Li; Hudson, Kreitman and Aguadé; and Tajima. The results of the analyses are displayed in tabular and graphic form.</p><p><strong>Availability: </strong>For academic uses, DnaSP is available via anonymous ftp: ftp.ebi.ac.uk in the directory/pub/software/dos.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 3","pages":"307-11"},"PeriodicalIF":0.0,"publicationDate":"1997-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20129981","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
Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. 用TREECON for Windows构建进化距离树:考虑位点间核苷酸取代率的变化。
Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01 DOI: 10.1093/bioinformatics/13.3.227
Y Van de Peer, R De Wachter
{"title":"Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites.","authors":"Y Van de Peer,&nbsp;R De Wachter","doi":"10.1093/bioinformatics/13.3.227","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.3.227","url":null,"abstract":"<p><strong>Motivation: </strong>To improve the estimation of evolutionary distances between nucleotide sequences by considering the differences in substitution rates among sites.</p><p><strong>Results: </strong>TREECON for Windows (Van de Peer,Y. and De Wachter,R. Comput. Applic. Biosci., 9, 569-570, 1994) is a software package for the construction and drawing of phylogenetic trees based on distance data computed from nucleic acid and amino acid sequences. For nucleic acids, we here describe the implementation of a recently developed method for estimating evolutionary distances taking into account the substitution rate of individual sites in a sequence alignment.</p><p><strong>Availability: </strong>TREECON for Windows is available on request from the authors. A small fee is asked in order to support the work and to reinvest in new computer hard- and software. More information about the program and substitution rate calibration can be found at URL http:/(/)bioc-www.uia.ac.be/u/ yvdp/treeconw.html.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 3","pages":"227-30"},"PeriodicalIF":0.0,"publicationDate":"1997-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.3.227","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20130106","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: 326
An iterative algorithm for converting a class II MHC binding motif into a quantitative predictive model. 将II类MHC结合基序转化为定量预测模型的迭代算法。
Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01 DOI: 10.1093/bioinformatics/13.3.211
R R Mallios
{"title":"An iterative algorithm for converting a class II MHC binding motif into a quantitative predictive model.","authors":"R R Mallios","doi":"10.1093/bioinformatics/13.3.211","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.3.211","url":null,"abstract":"<p><p>Biochemists and molecular biologists have suggested motifs for characterizing the binding of peptide fragments and class II major histocompatibility complex (MHC) molecules based on laboratory results and crystal structures. The iterative algorithm presented here converts a suggested motif into a quantitative data-based model. The database accessed consists of peptide fragments known to bind or not bind to class II MHC molecules of particular haplotypes. Stepwise discriminant analysis is utilized to increase or decrease motif coefficients until the resulting motif classifies all binders and non-binders correctly. Stepwise discriminant analysis is a standard multivariate statistical procedure and is available in comprehensive commercial statistical packages. Program 7M of BMDP Statistical Software was used in this study.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 3","pages":"211-5"},"PeriodicalIF":0.0,"publicationDate":"1997-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.3.211","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20130104","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: 4
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：604180095
Book学术官方微信