Database Redundancy Research Articles

Virtual machine optimization setting of ship public computer platform

Ship public computer platform is a shared platform built for ship users by using public hardware resources and equipment. Users of public computer platform can directly call the hardware resources of public computer platform through network, virtual machine and other media to create their own virtual computing environment. With the development of computer technology and virtualization technology, ship public computing platform technology has also received extensive attention in the industry. Firstly, this paper introduces the key points of cloud computing technology. Based on cloud platform computing, this paper introduces the virtual machine design, database redundancy design, CPU and network optimization setting of ship public computer platform in detail. Finally, the virtual machine construction of ship public computer platform is realized based on VMware software platform, which has very important application significance.

Identification of genus Campylobacter up to species level using internal features of 16S rRNA gene sequences

Introduction: 16S rRNA sequencing of novel isolates is one of the preliminary steps in characterization of bacteria, especially when the isolates are of medical relevance. The genus Campylobacter belongs to Class e-proteobacteria under the Phylum Proteobacteria. It represents economically important species which are gastrointestinal pathogens in humans and livestock animals. Currently, more than 400 16S rDNA sequences belonging to 28 species of this genus are present in the RDP database. But heterogeneity has led to the misplacement of many of these sequences within wrong species. Also, various sequences belonging to Campylobacter have been deposited as orphans. The current study aimed to explore the internal features of 16S rRNA gene sequences in order to develop methods for identification of Campylobacter up to species level. Methods: 428 16S rRNA sequences of 28 species of Campylobacter were analyzed. 392 sequences (>1200 nucleotides, nts) of 16 species were considered for (i) phylogenetic framework analysis and (ii) in silico restriction digestion. 28 uncharacterized sequences present in the database were also investigated in the present study. Results: Phylogenetic framework analysis allowed the identification of genetic variability within Campylobacter species and helped to segregate certain uncharacterized sequences up to species level. 12 out of the 16 species under study showed homogenous behavior, but heterogeneity was observed between C. jejuni and C. coli and C. helveticus and C. upsaliensis respectively. Unique restriction enzymes were identified for six species. Conclusions: The present approach clearly showed that internal features of 16S rRNA is a useful tool for characterization of novel isolates up to the species level. Studies have revealed that niche overlap and consequent increase in the horizontal gene transfer between C. coli and C. jejuni, due to anthropogenic factors, maybe the reason for their heterogeneous nature. This explains the difficulties faced in segregation of the members of these species. 16S rRNA gene proved to be a viable and excellent marker for characterizing the uncharacterized Campylobacter strains leading to a significant diminution in database redundancy. Further, the approaches used in the study might assist in easier identification of the various Campylobacter sequences present in the database.

Correction: Equivalent Indels - Ambiguous Functional Classes and Redundancy in Databases.

[This corrects the article DOI: 10.1371/journal.pone.0062803.].

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Equivalent indels--ambiguous functional classes and redundancy in databases.

There is considerable interest in studying sequenced variations. However, while the positions of substitutions are uniquely identifiable by sequence alignment, the location of insertions and deletions still poses problems. Each insertion and deletion causes a change of sequence. Yet, due to low complexity or repetitive sequence structures, the same indel can sometimes be annotated in different ways. Two indels which differ in allele sequence and position can be one and the same, i.e. the alternative sequence of the whole chromosome is identical in both cases and, therefore, the two deletions are biologically equivalent. In such a case, it is impossible to identify the exact position of an indel merely based on sequence alignment. Thus, variation entries in a mutation database are not necessarily uniquely defined. We prove the existence of a contiguous region around an indel in which all deletions of the same length are biologically identical. Databases often show only one of several possible locations for a given variation. Furthermore, different data base entries can represent equivalent variation events. We identified 1,045,590 such problematic entries of insertions and deletions out of 5,860,408 indel entries in the current human database of Ensembl. Equivalent indels are found in sequence regions of different functions like exons, introns or 5' and 3' UTRs. One and the same variation can be assigned to several different functional classifications of which only one is correct. We implemented an algorithm that determines for each indel database entry its complete set of equivalent indels which is uniquely characterized by the indel itself and a given interval of the reference sequence.

Uforia: Universal forensic indexer and analyzer

Uforia is a simple, flexible and extensible framework for analysis and parsing of file metadata. It has been written in Python and is available under the GPLv2. Uforia traverses a file-system and triggers a configurable set of modules for every file it encounters. Out-of-the-box, Uforia conforms to the NIST standard for forensic hashing by storing the currently most common three cryptographic hashes for each file: the MD5, SHA-1 and SHA-256 hash. Uforia strives for optimal scaling of the metadata-analysis by offering an easily configurable threading model of both its Producers and Consumers. Additionally, the interface is written and intended to be as loosely coupled as possible, as to easily reduce, replace or increase the Producer's and Consumer's functionalities to match the specific needs of the user. Uforia also attempts to reduce database redundancy to a minimum in the same way, by only loosely coupling database tables and delegating the relevant parts of the data-model to be handled by the individual modules. Each of these modules will perform its tasks asynchronously of Uforia and is automatically detected, registered and called to handle its specific filetypes. Uforia does not yet come with a front-end interface for viewing the information stored in the database, but the database contents stored could theoretically already be applied to a wide variety of situations, such as searching for specific metadata or information during a forensic investigation, for filesystem-level deduplication or even for creating custom known file hash tables. The interface for creating new database handlers and modules has been simplified as much as possible, allowing for easy extensibility and tailoring to each use-case's specific requirements.

The Comprehensive Gateway Model for Diverse Environmental Monitoring Upon Wireless Sensor Network

This study is aimed to establish a wireless sensor network (WSN) gateway model prior to the back-end server for diverse environmental monitoring applications. The design catalogs different sensor data with transmission load balance to incorporate heterogeneity of sensor signals, stability of data transportation, and expenditure of mobile communication. As considering a variety of sensor characteristics for environmental monitoring, the proposed WSN gateway is designed with three bridged functions, including serial listener, transaction logger and Internet listener, to enable analog and digital signal conversion, physical data classification, threshold determination, database redundancy and mobile communication. The criterion-based scheme is created for remotely updating thresholds of monitored data from the back-end server to the gateway. The model is built upon the embedded computer for low power consuming to perform efficient and stable applications. The comprehensive model design can be easily utilized for general WSN surveillance with expansibility and flexibility.

Comparison of Extensive Protein Fractionation and Repetitive LC-MS/MS Analyses on Depth of Analysis for Complex Proteomes

In-depth, reproducible coverage of complex proteomes is challenging because the complexity of tryptic digests subjected to LC-MS/MS analysis frequently exceeds mass spectrometer analytical capacity, which results in undersampling of data. In this study, we used cancer cell lysates to systematically compare the commonly used GeLC-MS/MS (1-D protein + 1-D peptide separation) method using four repetitive injections (2-D/repetitive) with a 3-D method that included solution isoelectric focusing and involved an equal number of LC-MS/MS runs. The 3-D method detected substantially more unique peptides and proteins, including higher numbers of unique peptides from low-abundance proteins, demonstrating that additional fractionation at the protein level is more effective than repetitive analyses at overcoming LC-MS/MS undersampling. Importantly, more than 90% of the 2-D/repetitive protein identifications were found in the 3-D method data in a direct protein level comparison, and the reproducibility between data sets increased to greater than 96% when factors such as database redundancy and use of rigid scoring thresholds were considered. Hence, high reproducibility of complex proteomes, such as human cancer cell lysates, readily can be achieved when using multidimensional separation methods with good depth of analysis.