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Developing Bioinformatics Computer Skills 发展生物信息学计算机技能
Computers & chemistry Pub Date : 2002-07-01 Epub Date: 2002-04-10 DOI: 10.1016/S0097-8485(02)00028-1
Jean-Loup Risler
{"title":"Developing Bioinformatics Computer Skills","authors":"Jean-Loup Risler","doi":"10.1016/S0097-8485(02)00028-1","DOIUrl":"10.1016/S0097-8485(02)00028-1","url":null,"abstract":"","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 5","pages":"Pages 553-555"},"PeriodicalIF":0.0,"publicationDate":"2002-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(02)00028-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76433108","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
Grand metaphors of biology in the genome era 基因组时代生物学的伟大隐喻
Computers & chemistry Pub Date : 2002-07-01 Epub Date: 2002-04-11 DOI: 10.1016/S0097-8485(02)00024-4
Andrzej K Konopka
{"title":"Grand metaphors of biology in the genome era","authors":"Andrzej K Konopka","doi":"10.1016/S0097-8485(02)00024-4","DOIUrl":"10.1016/S0097-8485(02)00024-4","url":null,"abstract":"","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 5","pages":"Pages 397-401"},"PeriodicalIF":0.0,"publicationDate":"2002-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(02)00024-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90275132","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: 29
Genome compartimentation by a Hybrid Chromosome Model (HχM). Application to Saccharomyces cerevisae subtelomeres 杂交染色体模型的基因组比较(HχM)。酿酒酵母亚端粒的应用
Computers & chemistry Pub Date : 2002-07-01 Epub Date: 2002-01-29 DOI: 10.1016/S0097-8485(02)00006-2
Alexandre G. de Brevern , France Loirat , Anne Badel-Chagnon , Cécile André , Pierre Vincens , Serge Hazout
{"title":"Genome compartimentation by a Hybrid Chromosome Model (HχM). Application to Saccharomyces cerevisae subtelomeres","authors":"Alexandre G. de Brevern ,&nbsp;France Loirat ,&nbsp;Anne Badel-Chagnon ,&nbsp;Cécile André ,&nbsp;Pierre Vincens ,&nbsp;Serge Hazout","doi":"10.1016/S0097-8485(02)00006-2","DOIUrl":"10.1016/S0097-8485(02)00006-2","url":null,"abstract":"<div><p>The aim of this paper is to present a new approach, called ‘Hybrid Chromosome Model’ (HχM), which allows both the extraction of regions of similarity between two sequences, and the compartimentation of a set of DNA sequences. The principle of the method consists in compacting a set of sequences (split into fragments of fixed length) into a ‘hybrid chromosome’, which results from the stacking of the whole sequence fragments. We have illustrated our approach on the 32 subtelomeres of <em>Saccharomyces cerevisae</em>. The compartimentation of these chromosome extremities into common regions of similarity has been carried out. The approach HχM is a fast and efficient tool for mapping entire genomes and for extracting ancient duplications within or between genomes.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 5","pages":"Pages 437-445"},"PeriodicalIF":0.0,"publicationDate":"2002-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(02)00006-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82419633","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
This Is Biology: The Science of the Living World 这是生物学:生命世界的科学
Computers & chemistry Pub Date : 2002-07-01 Epub Date: 2002-04-12 DOI: 10.1016/S0097-8485(02)00025-6
Andrzej K Konopka
{"title":"This Is Biology: The Science of the Living World","authors":"Andrzej K Konopka","doi":"10.1016/S0097-8485(02)00025-6","DOIUrl":"10.1016/S0097-8485(02)00025-6","url":null,"abstract":"","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 5","pages":"Pages 543-545"},"PeriodicalIF":0.0,"publicationDate":"2002-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(02)00025-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83438036","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: 6
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins 生物信息学:基因和蛋白质分析的实用指南
Computers & chemistry Pub Date : 2002-07-01 Epub Date: 2002-04-10 DOI: 10.1016/S0097-8485(02)00027-X
Jean-Loup Risler
{"title":"Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins","authors":"Jean-Loup Risler","doi":"10.1016/S0097-8485(02)00027-X","DOIUrl":"10.1016/S0097-8485(02)00027-X","url":null,"abstract":"","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 5","pages":"Pages 549-551"},"PeriodicalIF":0.0,"publicationDate":"2002-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(02)00027-X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84741377","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
Applications of recursive segmentation to the analysis of DNA sequences 递归分割在DNA序列分析中的应用
Computers & chemistry Pub Date : 2002-07-01 Epub Date: 2002-01-29 DOI: 10.1016/S0097-8485(02)00010-4
Wentian Li , Pedro Bernaola-Galván , Fatameh Haghighi , Ivo Grosse
{"title":"Applications of recursive segmentation to the analysis of DNA sequences","authors":"Wentian Li ,&nbsp;Pedro Bernaola-Galván ,&nbsp;Fatameh Haghighi ,&nbsp;Ivo Grosse","doi":"10.1016/S0097-8485(02)00010-4","DOIUrl":"10.1016/S0097-8485(02)00010-4","url":null,"abstract":"<div><p>Recursive segmentation is a procedure that partitions a DNA sequence into domains with a homogeneous composition of the four nucleotides A, C, G and T. This procedure can also be applied to any sequence converted from a DNA sequence, such as to a binary strong(G+C)/weak(A+T) sequence, to a binary sequence indicating the presence or absence of the dinucleotide CpG, or to a sequence indicating both the base and the codon position information. We apply various conversion schemes in order to address the following five DNA sequence analysis problems: isochore mapping, CpG island detection, locating the origin and terminus of replication in bacterial genomes, finding complex repeats in telomere sequences, and delineating coding and noncoding regions. We find that the recursive segmentation procedure can successfully detect isochore borders, CpG islands, and the origin and terminus of replication, but it needs improvement for detecting complex repeats as well as borders between coding and noncoding regions.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 5","pages":"Pages 491-510"},"PeriodicalIF":0.0,"publicationDate":"2002-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(02)00010-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79853764","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: 105
Modeling comparative mapping using objects and associations 使用对象和关联建模比较映射
Computers & chemistry Pub Date : 2002-07-01 Epub Date: 2002-01-29 DOI: 10.1016/S0097-8485(02)00004-9
G Bronner , B Spataro , M Page , C Gautier , F Rechenmann
{"title":"Modeling comparative mapping using objects and associations","authors":"G Bronner ,&nbsp;B Spataro ,&nbsp;M Page ,&nbsp;C Gautier ,&nbsp;F Rechenmann","doi":"10.1016/S0097-8485(02)00004-9","DOIUrl":"10.1016/S0097-8485(02)00004-9","url":null,"abstract":"<div><p>Spatial information on genome organization is essential for both gene prediction and annotation among species and a better understanding of genomes functioning and evolution. We propose in this article an object-association model to formalize comparative genomic mapping. This model is being implemented in the GeMCore knowledge base, for which some original capabilities are described. GeMCore associated to the GeMME graphical interface for molecular evolution was used to spatially characterize the minor shift phenomenon between human and mouse.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 5","pages":"Pages 413-420"},"PeriodicalIF":0.0,"publicationDate":"2002-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(02)00004-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78169809","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
Pairwise sequence alignment using a PROSITE pattern-derived similarity score 使用PROSITE模式衍生的相似性评分的两两序列比对
Computers & chemistry Pub Date : 2002-07-01 Epub Date: 2002-01-30 DOI: 10.1016/S0097-8485(02)00005-0
J.-P. Comet , J. Henry
{"title":"Pairwise sequence alignment using a PROSITE pattern-derived similarity score","authors":"J.-P. Comet ,&nbsp;J. Henry","doi":"10.1016/S0097-8485(02)00005-0","DOIUrl":"10.1016/S0097-8485(02)00005-0","url":null,"abstract":"<div><p>Existing methods for alignments are based on edition costs computed additionally position by position, according to a fixed substitution matrix: a substitution always has the same weight regardless of the position. Nevertheless the biologist favours a similarity according to his knowledge of the structure or the function of the sequences considered. In the particular case of proteins, we present a method consisting in integrating other information, such as patterns of the PROSITE databank, in the classical dynamic programming algorithm. The method consists in making an alignment by dynamic programming taking a decision not only letter by letter as in the Smith &amp; Waterman algorithm but also by giving a reward when aligning patterns.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 5","pages":"Pages 421-436"},"PeriodicalIF":0.0,"publicationDate":"2002-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(02)00005-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83782343","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: 16
Strategies for the identification, the assembly and the classification of integrated biological systems in completely sequenced genomes 在完全测序的基因组中鉴定、组装和分类整合生物系统的策略
Computers & chemistry Pub Date : 2002-07-01 Epub Date: 2002-01-25 DOI: 10.1016/S0097-8485(02)00007-4
Yves Quentin , Julie Chabalier , Gwennaele Fichant
{"title":"Strategies for the identification, the assembly and the classification of integrated biological systems in completely sequenced genomes","authors":"Yves Quentin ,&nbsp;Julie Chabalier ,&nbsp;Gwennaele Fichant","doi":"10.1016/S0097-8485(02)00007-4","DOIUrl":"10.1016/S0097-8485(02)00007-4","url":null,"abstract":"<div><p>The proteins involved in a single biological process may form a stable supra-molecular assembly or be transiently in interaction. Although, the first annotation steps of a complete genome may allow the identification of the different partners, their assembly in a functional system, referred to as an integrated system, is a domain where methodological effort has to be done. Indeed, the knowledge required to assemble partners of such systems should be explicitly included in annotation software. The availability of a complete genome, and therefore of all the proteins encoded by that genome, motivated the development of automated approaches through the coordinated combination of different bio-informatic methods allowing the identification of the different partners, their assembly and the classification of the reconstructed systems in functional categories. In this data flux, the identification of the sequence partners represents the principal bottleneck. Here, we describe and compare the results obtained with different classes of methods (<span>blastp2</span>, <span>psi</span>-<span>blast</span>, <span>mast</span> and M<span>eta</span>-<span>meme</span>) applied to the identification in complete genomes of a given family of integrated systems: the ABC transporters. <span>psi</span>-<span>blast</span> appears to significantly outperform motif-based methods, and the results are discussed according to the nature of the proteins and the structure of the sub-families.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 5","pages":"Pages 447-457"},"PeriodicalIF":0.0,"publicationDate":"2002-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(02)00007-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84279598","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
Local weighting schemes for protein multiple sequence alignment 蛋白质多序列比对的局部加权方法
Computers & chemistry Pub Date : 2002-07-01 Epub Date: 2002-01-29 DOI: 10.1016/S0097-8485(02)00008-6
Jaap Heringa
{"title":"Local weighting schemes for protein multiple sequence alignment","authors":"Jaap Heringa","doi":"10.1016/S0097-8485(02)00008-6","DOIUrl":"10.1016/S0097-8485(02)00008-6","url":null,"abstract":"<div><p>This paper describes three weighting schemes for improving the accuracy of progressive multiple sequence alignment methods: (1) global profile pre-processing, to capture for each sequence information about other sequences in a profile before the actual multiple alignment takes place; (2) local pre-processing; which incorporates a new protocol to only use non-overlapping local sequence regions to construct the pre-processed profiles; and (3) local–global alignment, a weighting scheme based on the double dynamic programming (DDP) technique to softly bias global alignment to local sequence motifs. The first two schemes allow the compilation of residue-specific multiple alignment reliability indices, which can be used in an iterative fashion. The schemes have been implemented with associated iterative modes in the PRALINE multiple sequence alignment method, and have been evaluated using the BAliBASE benchmark alignment database. These tests indicate that PRALINE is a toolbox able to build alignments with very high quality. We found that local profile pre-processing raises the alignment quality by 5.5% compared to PRALINE alignments generated under default conditions. Iteration enhances the quality by a further percentage point. The implications of multiple alignment scoring functions and iteration in relation to alignment quality and benchmarking are discussed.</p></div>","PeriodicalId":79331,"journal":{"name":"Computers & chemistry","volume":"26 5","pages":"Pages 459-477"},"PeriodicalIF":0.0,"publicationDate":"2002-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0097-8485(02)00008-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73167550","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: 49
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