Logol : Modelling evolving sequence families through a dedicated constrained string language
نویسندگان
چکیده
The report reviews the key milestones that have been reached so far in applying formal languages to the analysis of genomic sequences. Then it introduces a new modelling language, Logol, that aims at expressing more easily complex structures on genomic sequences. It is based on a development of String Variable Grammars, a formal framework proposed by D. Searls. Key-words: Bioinformatics, Sequence Modelling, Formal languages, Logical Grammars, Constraints, String variable Logol : modéliser l’évolution de familles de séquences biologiques au moyen d’un langage dédié à base de contraintes Résumé : Ce document concerne l’utilisation de langages formels au service de la modélisation de séquences génomiques. Dans un premier temps, une étude des travaux fondateurs sur ce sujet est développée. Ensuite, un nouveau langage de modélisation, Logol, est présenté. Logol vise à exprimer plus facilement des structures complexes sur des séquences génomiques. Il est basé sur un développement des grammaires à variable de châınes (SVG), structure formelle proposée par David Searls pour la modélisation biologique. Mots-clés : Bioinformatique, modélisation de séquences, langages formels, grammaires logiques, contraintes, variables de chanes Logol: a constrained string language for sequence modelling 3
منابع مشابه
A Koala-Based Approach for Modelling and Deploying Configurable Software Product Families
An approach for modelling configurable software product families (CSPFs) and for automated configuring of product individuals using the models is presented. It is based on a similar approach for configuring physical products. The conceptual foundation and syntax of the Koalish modelling language used for this purpose are defined. The language extends Koala, a component model and architecture de...
متن کاملA THEORETICALLY CORRECT RESOURCE USAGE VISUALIZATION FOR THE RESOURCE-CONSTRAINED PROJECT SCHEDULING PROBLEM
The cumulative resource constraints of the resource-constrained project scheduling problem (RCPSP) do not treat the resource demands as geometric rectangles, that is, activities are not necessarily assigned to the same resource units over their processing times. In spite of this fact, most papers on resource-constrained project scheduling mainly in the motivation phase use a strip packing of re...
متن کاملPCL: a language for modelling evolving system architectures
The paper describes a language called PCL, which has been designed to model the architecture of multiple versions of computer-based systems (system families). PCL has evolved from module interconnection languages, and its novel features include the ability to model the variability between members of a system family and facilities for the integrated modelling of hardware, software and documentat...
متن کاملA Cuckoo search algorithm (CSA) for Precedence Constrained Sequencing Problem (PCSP)
Precedence constrained sequencing problem (PCSP) is related to locate the optimal sequence with the shortest traveling time among all feasible sequences. In PCSP, precedence relations determine sequence of traveling between any two nodes. Various methods and algorithms for effectively solving the PCSP have been suggested. In this paper we propose a cuckoo search algorithm (CSA) for effectively ...
متن کاملGrammar string: a novel ncRNA secondary structure representation
Multiple ncRNA alignment has important applications in homologous ncRNA consensus structure derivation, novel ncRNA identification, and known ncRNA classification. As many ncRNAs’ functions are determined by both their sequences and secondary structures, accurate ncRNA alignment algorithms must maximize both sequence and structural similarity simultaneously, incurring high computational cost. F...
متن کامل