The Open Applied Informatics Journal最新文献

{"title":"Moving Target Search Algorithm with Informational Distance Measures","authors":"E. Kagan, I. Ben-Gal","doi":"10.2174/1874136320130604001","DOIUrl":"https://doi.org/10.2174/1874136320130604001","url":null,"abstract":"We consider an Ishida and Korf Moving Target Search (MTS) algorithm with informational distance measures. Similarly to the previously defined Informational Learning Real-Time A* algorithm, the suggested algorithm acts on the set of partitions of the sample space, on which the probability mass function is defined. The information-based Rokhlin metric and its lower bound - Ornstein metric, give the necessary distance measures. We prove that similarly to the Ishida and Korf MTS algorithm, the proposed Informational MTS (IMTS) algorithm always terminates and finds the target. The comparison of the IMTS algorithm with known models shows that it outperforms known Markov decision process model of search with probabilistic and informational decision criteria. These findings help to construct a unified framework of search after both static and moving targets, and to bridge the gap between different search procedures that are related to both artificial intelligence and information theory.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128182610","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 Multidisciplinary Approach to the Microbial Species Concept: The Role of Bioinformatics in the Search of Detectable Discontinuities","authors":"Livio Antonielli, L. Corte, L. Roscini, V. Robert, Ambra Bagnetti, F. Fatichenti, G. Cardinali","doi":"10.2174/1874136301105010003","DOIUrl":"https://doi.org/10.2174/1874136301105010003","url":null,"abstract":"The problem of species and in particular microbial species is central in biology. An active collaboration of various specialists such as taxonomists, epistemologists, mathematicians and bioinformatics experts is desirable for its solution. This article intended to show the possibilities and perspectives of bioinformatics research in understanding the ontological problem of species, i.e. the problem of the existence of the microbial species. The approach undertaken of this paper is based on the concept that if microbial species exist, then there should be detectable discontinuities or disconnections between microorganisms assigned to different species. A yeast model has been used to show how the distances from a reference organism raise with the increase of the number of different strains included in the study.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127864417","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":"Molecular Identification of Fungi: Rationale, Philosophical Concerns, and the UNITE Database","authors":"R. H. Nilsson, K. Abarenkov, K.-H. Larsson, U. Kõljalg","doi":"10.2174/1874136301105010081","DOIUrl":"https://doi.org/10.2174/1874136301105010081","url":null,"abstract":"Fungi form a ubiquitous group of largely inconspicuous organisms that play key ecological roles in terrestrial nutrient cycling. The typically subterranean or otherwise unnoticeable nature of fungal life has left mycology with a partial understanding of fungal biology, and progress is hampered by factors such as the difficulty to delimit species and individuals of fungi and the sparsity of discriminatory morphological and physiological characters for reliable species identification. These and other complications have paved the way for DNA sequence data as an important source of information in mycology, and there are now twenty years' worth of fungal sequence data available for scientific purposes. However, issues of data reliability and generality impede the use of publicly available fungal DNA sequences. The UNITE database for molecular identification of fungi (http://unite.ut.ee) was built as a response to the difficulties facing anyone seeking to identify environmental samples of fungi to species level using molecular data and the major international sequence databases. The present study describes the UNITE database and examines the role of UNITE in the light of emerging sequencing technologies, notably massively parallel (\"454\") pyrosequencing. Environmental sampling of fungi is discussed from a taxonomic perspective.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"83 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122181129","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":"Assessing the Potential of FT-IR to Identify Clinical Strains of Candida spp.","authors":"Filipa Brandão, C. Veríssimo, J. Brandão","doi":"10.2174/1874136301105010077","DOIUrl":"https://doi.org/10.2174/1874136301105010077","url":null,"abstract":"clinical isolates of Candida spp were examined by FT-IR in order to compare identification using FT-IR with biochemical identification (bioMerieux ® ). FT-IR revealed itself as a fast and effective method for identification of the strains tested as all were placed into the appropriate species, including one which was misidentified by the biochemical method.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"57 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121223021","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":"Recognition of Yeast Species from Gene Sequence Comparisons","authors":"C. Kurtzman","doi":"10.2174/1874136301105010020","DOIUrl":"https://doi.org/10.2174/1874136301105010020","url":null,"abstract":"This review discusses recognition of yeast species from gene sequence comparisons, which have been responsible for doubling the number of known yeasts over the past decade. The resolution provided by various single gene sequences is examined for both ascomycetous and basidiomycetous species, and the greater resolution of species provided by multigene analyses is discussed. Various methods are presented for rapid species identification using gene sequences.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"59 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125929983","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":"BioloMICS Software: Biological Data Management, Identification, Classification and Statistics","authors":"V. Robert, S. Szoke, B. Jabas, D. Vu, O. Chouchen, Erik Blom, G. Cardinali","doi":"10.2174/1874136301105010087","DOIUrl":"https://doi.org/10.2174/1874136301105010087","url":null,"abstract":"The BioloMICS software is briefly described in this application note. BioloMICS is a tool allowing specialized and scientific biological databases to be created to fit the specific needs of researchers working on any organisms (from viruses, bacteria, fungi, plants, insects to animals) by abroad base of users such as taxonomists, ecologists, human, animal or plant pathologists, molecular biologists, pharmacists, industrial researchers, etc. They can all use the system in completely different ways and with different goals in mind. One can create own custom databases without any prior knowledge of either databasing or programming. The system is completely dynamic and can evolve with the needs of the users. A number of tools for data retrieval and analysis are also included in the system. The system also allows linking with many other databases. BioloMICS is proposed as a suite of tools capable of archiving, analyzing and publishing data on local computers and Internet servers.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124406538","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":"Centrality of Objects in a Multidimensional Space and its Effects on Distance-Based Biological Classifications","authors":"Livio Antonielli, V. Robert, L. Corte, L. Roscini, R. Ceppitelli, G. Cardinali","doi":"10.2174/1874136301005010011","DOIUrl":"https://doi.org/10.2174/1874136301005010011","url":null,"abstract":"Typology is based on the concept that one individual (the type) can represent the whole group. In yeast taxonomy the type strain is the representative of the whole species and is considered an important tool for classification. Although the evolutionary, phylogenetic and biological species concepts are in contrast with this approach, the International Codes of nomenclature still use typology, which remains one of the most operative systems. These incongruities demand a multidisciplinary investigation on the nature of the type, its characteristics and the possibility of the type to be defined on the basis of a shareable criterion. In this paper we present an approach to the problem of type centrality based on mathematical demonstrations and numerical examples. This paper intended to show the possibilities offered to bioinformatics research by the implementation of multidisciplinary approaches in biology and in proposing a general approach to the definition of the type representing any sort of set, described with multiple descriptors.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116690326","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":"Editorial - Bioinformatics as an Increasingly Important Resource in Taxonomy, Phylogenetic and Diagnostics","authors":"G. Cardinali, V. Robert","doi":"10.2174/1874136301105010001","DOIUrl":"https://doi.org/10.2174/1874136301105010001","url":null,"abstract":"This special Issue on Bioinformatics as an Increasingly Important Resource in Taxonomy, Phylogenetic and Diagnostics is an attempt to emphasize the importance of a multidisciplinary approach to these complex branches of Biology. Taxonomy and Systematics deal with classification of biological groups, mainly at the species level. Phylogeny tries to reconstruct the most likely history of species. Diagnostics is a discipline that takes advantage of all the classificatory knowledge to individuate rapidly and precisely the species of interest, especially in clinical environments. The core object of all these activities is the species on which a debate exists to determine whether it is as mere conventional categories or as real structure and, more generally, to produce a largely shared species concept. This concept is even more complex in Microbiology, a relatively young science which has often taken concepts, definitions and operations from general Biology, although we are now aware of the deep difference between the genetic determinants in Microbiology and in the rest of Biology. The presence of massive horizontal gene transfer, the short time interval between mutation and selection, the fact that many microbes are haploid and then all mutations are immediately selectable, the possibility to reproduce asexually or with a sexuality which often trespasses the possible boundaries of the species, are some of the many problems the microbiologist deal with in their everyday struggle to catalog microbial biodiversity and to understand its structure. Every classification relies on a theory, or is a theory itself and gives the framework for the elaboration of new theories. The classification is therefore not important only for its mere practical outcomes, but rather for its deep scientific meaning and for the possibility it offers for the advancement of Science. This simple outline of the problems involved in classification gives an idea of the specialties necessary to gain deeper comprehension on microbial evolution and to define optimal systems for classification and identification. This special issue opens with two papers on two basic concepts involved in every biological, but especially in microbial classification: the problems of the continuity of taxa and of the centrality of the type strains. Although Phylogenetic has long disregarded typology as a form of classification, the International Codes regulating microbial systematics are strongly based on a typological design, implying that indeed types exist and that they are meaningful. Cardinali and coworkers investigate on the statistical and bioinformatics tools to ascertain if discontinuities separate …","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"501 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125932530","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":"Identification of Fungal DNA Barcode Targets and PCR Primers Based on Pfam Protein Families and Taxonomic Hierarchy","authors":"C. Lewis, S. Bilkhu, V. Robert, U. Eberhardt, S. Szoke, K. Seifert, C. Lévesque, Agri-food Canada","doi":"10.2174/1874136301105010030","DOIUrl":"https://doi.org/10.2174/1874136301105010030","url":null,"abstract":"DNA barcoding is the application of DNA sequences of standardized genetic markers for the identification of eukaryotic organisms. We attempted to identify alternative candidate barcode gene targets for the fungal biota from available fungal genomes using a taxonomy-aware processing pipeline. Putative-protein coding sequences were matched to Pfam protein families and aligned to reference Pfam accessions. Conserved sequence blocks were identified in the resulting alignments and degenerate primers were designed. The processing pipeline is described and the resulting candidate gene targets are discussed. The pipeline allows analysis of subsets at various hierarchical, taxonomic levels (selectable by GenBank taxonomy ID or scientific name) of the available reference data, allowing discrete taxonomic groups to be combined into a single subset, or for subordinate taxa to be excluded from the analysis of higher-level taxa. Putative degenerate primer pairs were designed as high as the superkingdom rank for the set of organisms included in the analysis. The identified targets have essential housekeeping functions, like the well known phylogenetic or barcode markers, and most have a better resolution potential to differentiate species among fully sequenced genomes than the most presently used markers. Some of the commonly used species-level phylogenetic markers for fungi, especially tef1-� and rpb2, were not recovered in our analysis because of their existence in multiple copies in single organisms, and because Pfam families do not always correlate with complete proteins.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128275850","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 Gene Flow between Plasmids and Chromosomes: Insights from Bioinformatics Analyses","authors":"Isabel Maida, M. Fondi, M. C. Papaleo, Elena Perrin, R. Fani","doi":"10.2174/1874136301105010062","DOIUrl":"https://doi.org/10.2174/1874136301105010062","url":null,"abstract":"Despite the key-role of plasmids in the horizontal spreading of genetic information within the prokaryotic community, their evolutionary dynamics has been poorly explored. Recently, a computational pipeline (Blast2Network) based on similarity networks reconstruction has been developed. Adopting this strategy we analyzed the genome of Synechococcus sp. PCC 7002, a cyanobacterium that possesses six plasmids and one chromosome and that can be considered as a model microorganism to analyze the interrelationships existing between different plasmids and between plasmids and chromosome. The aims of our work were: i) the identification and the analysis of the possible evolutionary relationships existing within and among the six Synechococcus sp. PCC 7002 plasmids at both intra- and intermolecular level, ii) the analysis of the gene flow (if any) existing between chromosome and plasmids of different size inhabiting the same cytoplasm. A deep analysis of the obtained networks suggested that i) intra-molecular rearrangements did not occur very recently in evolution of plasmids; ii) evolutionary relationships exist between both plasmids and plasmids and chromosome; iii) these exchanges may involve a single gene, operons or gene clusters. Besides, the overall degree of sequence identity/similarity shared by interconnected proteins suggests that plasmids are more prone to recombine between them rather than with chromosome.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"55 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127695872","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}