{"title":"Formal language theory and biological macromolecules","authors":"D. Searls","doi":"10.1090/dimacs/047/06","DOIUrl":"https://doi.org/10.1090/dimacs/047/06","url":null,"abstract":"Biological macromolecules can be viewed, at one level, as strings of symbols. Collections of such molecules can thus be considered to be sets of strings, i.e. formal languages. This article reviews language-theoretic approaches to describing intramolecular and intermolecular structural interactions within these molecules, and evolutionary relationships between them.","PeriodicalId":175691,"journal":{"name":"Mathematical Support for Molecular Biology","volume":"94 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127265984","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}
{"title":"A simple toolkit for DNA fragment assembly","authors":"J. Meidanis","doi":"10.1090/dimacs/047/14","DOIUrl":"https://doi.org/10.1090/dimacs/047/14","url":null,"abstract":"","PeriodicalId":175691,"journal":{"name":"Mathematical Support for Molecular Biology","volume":"20 3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127562808","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}
{"title":"The topologically driven strand separation transition in DNA - methods of analysis and biological significance","authors":"C. Benham","doi":"10.1090/dimacs/047/08","DOIUrl":"https://doi.org/10.1090/dimacs/047/08","url":null,"abstract":"","PeriodicalId":175691,"journal":{"name":"Mathematical Support for Molecular Biology","volume":"154 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132726605","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}
L. Milanesi, M. Marsilli, G. Mauri, C. Rolfi, L. Uboldi
{"title":"Fragment assembly system for DNA sequencing projects","authors":"L. Milanesi, M. Marsilli, G. Mauri, C. Rolfi, L. Uboldi","doi":"10.1090/dimacs/047/12","DOIUrl":"https://doi.org/10.1090/dimacs/047/12","url":null,"abstract":"","PeriodicalId":175691,"journal":{"name":"Mathematical Support for Molecular Biology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132224033","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}
{"title":"Sequence alignment and phylogeny construction","authors":"M. Vingron","doi":"10.1090/dimacs/047/03","DOIUrl":"https://doi.org/10.1090/dimacs/047/03","url":null,"abstract":"","PeriodicalId":175691,"journal":{"name":"Mathematical Support for Molecular Biology","volume":"71 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114804634","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}
{"title":"Sequence alignment in molecular biology","authors":"A. Apostolico, R. Giancarlo","doi":"10.1090/dimacs/047/05","DOIUrl":"https://doi.org/10.1090/dimacs/047/05","url":null,"abstract":"Molecular biology is a computationally intense realm of contemporary science and faces some of the current grand scientific challenges. In its context, tools that identify, store, compare and analyze effectively large and growing numbers of bio-sequences are found of increasingly crucial importance. Biosequences are routinely compared or aligned, in a variety of ways, to infer common ancestry, to detect functional equivalence, or simply while searching for similar entries in a database. A considerable body of knowledge has accumulated on sequence alignment during the past few decades. Without pretending to be exhaustive, this paper attempts a survey of some criteria of wide use in sequence alignment and comparison problems, and of the corresponding solutions. The paper is based on presentations and literature given at the Workshop on Sequence Alignment held at Princeton, N.J., in November 1994, as part of the DIMACS Special Year on Mathematical Support for Molecular Biology. \"Dipartimento di Elettronica e Informatica, Universita. di Padova, Via Gradenigo 6/A, 35131 Padova, Italy, (3949)828-7710; axa@arLdei.unipd.iti partially supported by NSF grant CCR_92_01078, by NATO grant CRG 900293, by the National Research Council of Italy, and by the ESPRIT III Basic Research Programme of the EC under contract No. 9072 (Project GEPPCOM). IDipartimento di Matcmatica, University of Palermo, Via Archirafi 34, 90123 Palermo, ItalYi raffaelc@altair.math.unipa.it; partially supported by MURST Grant \"Algoritmi, Strutture di Calcolo e Sistemi Informativin; part of this work was done while the author was visiting AT&T Bell Labs., Murray Hill, NJ. > U.S.A..","PeriodicalId":175691,"journal":{"name":"Mathematical Support for Molecular Biology","volume":"56 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121706651","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}
{"title":"Visualizing measures of genetic distance","authors":"Eric M. Jordan","doi":"10.1090/dimacs/047/11","DOIUrl":"https://doi.org/10.1090/dimacs/047/11","url":null,"abstract":"","PeriodicalId":175691,"journal":{"name":"Mathematical Support for Molecular Biology","volume":"112 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128002860","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}
{"title":"Performance of the CAP2 sequence assembly program","authors":"Xiaoqiu Huang","doi":"10.1090/dimacs/047/13","DOIUrl":"https://doi.org/10.1090/dimacs/047/13","url":null,"abstract":"","PeriodicalId":175691,"journal":{"name":"Mathematical Support for Molecular Biology","volume":"53 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125681021","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}
{"title":"A column-generation based branch-and-bound algorithm for sorting by reversals","authors":"A. Caprara, G. Lancia, See-Kiong Ng","doi":"10.1090/dimacs/047/10","DOIUrl":"https://doi.org/10.1090/dimacs/047/10","url":null,"abstract":"We consider the problem of sorting a permutation by reversals (SBR), calling for the minimum number of reversals transforming a given permutation of f1; : : : ; ng into the identity permutation. SBR was inspired by computational biology applications , in particular genome rearrangement. We propose an exact branch-and-bound algorithm for SBR. A lower bound is computed by solving a linear program with a possibly exponential (in n) number of variables, by using column generation techniques. An eeective branching scheme is described, which is combined with a greedy algorithm capable of producing near{optimal solutions. The algorithm presented can solve to optimality SBR instances of considerably larger size with respect to previous existing methods.","PeriodicalId":175691,"journal":{"name":"Mathematical Support for Molecular Biology","volume":"52 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123656030","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}
{"title":"An introduction to molecular biology for mathematicians and computer programmers","authors":"W. Fitch","doi":"10.1090/dimacs/047/01","DOIUrl":"https://doi.org/10.1090/dimacs/047/01","url":null,"abstract":"","PeriodicalId":175691,"journal":{"name":"Mathematical Support for Molecular Biology","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126950980","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}
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
