Virusite—integrated database for viral genomics

Viruses are the most abundant biological entities and the reservoir of most of the genetic diversity in the Earth’s biosphere. Database works Viral genomes are very diverse, generally short in length and compared to other organisms carry only few genes. Data recovery cheap viruSITE is a novel database which brings together high-value information compiled from various resources.


Database of state incentives for renewables and efficiency viruSITE covers the whole universe of viruses and focuses on viral genomes, genes and proteins. Data recovery usb stick The database contains information on virus taxonomy, host range, genome features, sequential relatedness as well as the properties and functions of viral genes and proteins. Database companies All entries in the database are linked to numerous information resources. Database application The above-mentioned features make viruSITE a comprehensive knowledge hub in the field of viral genomics. The web interface of the database was designed so as to offer an easy-to-navigate, intuitive and user-friendly environment. Database online It provides sophisticated text searching and a taxonomy-based browsing system. Database high availability viruSITE also allows for an alternative approach based on sequence search. Database utility A proprietary genome browser generates a graphical representation of viral genomes. Data recovery zagreb In addition to retrieving and visualising data, users can perform comparative genomics analyses using a variety of tools. Viruses are the simplest biological forms bordering on the edge between living and non-living. Database javascript Nevertheless, their genomes are more diverse than any other forms of life. Database administrator jobs Viral genomes vary in terms of their length (from 1.7 kb of circoviruses to 2500 kb of Pandoravirus salinus), composition (ssRNA, dsRNA, ssDNA and dsDNA), topology (linear, circular) and consist of a single strand or multiple segments of nucleic acid ( 1). Data recovery for iphone A common feature of all viral genomes is their small size (mostly <50 kb) and high density of gene coding regions (mostly >90%). Genomes of viruses (bacteriophages MS2 and phiX174) were the first to be sequenced ( 2, 3). Data recovery victoria bc At present, there are thousands of known viral genome sequences. 10k database The NCBI Viral Genomes Resource contains over 5600 complete reference viral genomes ( http://www.ncbi.nlm.nih.gov/genomes/Genom esGroup.cgi?taxid=10239). Data recovery software mac In total, >2 million sequences of viral origin are deposited in INSDC databases ( http://www.ncbi.nlm.nih.gov/nuccore/?term= txid10239[Organism:exp]). Cost of data recovery from hard drive Next-generation sequencing technology brought a rapid increase in sequenced genomes and established new challenges associated with annotating and maintaining viral genomes ( 4). There are various public databases which store and distribute information regarding viral genome sequences, annotation of genes and proteins, information on viral structure, biology, pathology and taxonomy. S cerevisiae database Primary sequence databases, INSDC databases (GenBank/ENA/DDBJ) ( 5) and Uniprot ( 6) constitute the main repositories of sequence data concerning nucleotide and protein levels. Snl database ViralZone is a curated virus knowledge base which focuses on molecular biology of viruses, virion structure, genome, replication cycle, host range, geographical distribution and epidemiology ( 7). Database 4500 ViPR is an integrated data repository which provides tools for analysis of human pathogenic viruses ( 8). Data recovery miami fl Reports of the International Committee on the Taxonomy of Viruses (ICTV) ( 9) are considered both the standard and the reference for the taxonomy of viruses. Data recovery sd card The taxonomy releases are also available online ( www.ictvonline.org). Uottawa database Furthermore, there are databases focusing on specific groups of viruses, e.g. Top 10 data recovery software free download OpenFluDB ( 10), Ebola Virus Knowledgebase ( 11), HBVdb ( 12) and many others. With the aim to create a broader annotation system for genomes, genes and proteins encompassing the whole universe of viruses, the data were collected from several resources. Database query optimization All genome sequences in viruSITE were extracted from all reference viral genomes deposited in the NCBI RefSeq database (records with ‘NC_’ accession prefix). Qmobile data recovery The annotation acquired from the RefSeq entries was amended with the data obtained from UniProtKB, Pfam, GO, ViralZone, NCBI Taxonomy and PubMed. No 1 data recovery software All the data were downloaded, parsed, pre-computed, combined and inserted into the database using in-house developed scripts. Data recovery iphone free All scripts work semi-automatically, and therefore human supervision is necessary. The database is regularly updated (at least two releases per year). Database 11g Since 2013, when viruSITE was established, the total number of records has doubled. Data recovery thumb drive The current release (2016.2) contains records for 5633 viruses, viroids and satellites (7312 genome sequences in total), 273 366 records for genes and 269 157 records for proteins. Data recovery hardware tools The content of the database is available to everyone for any purpose and it is distributed under the ‘Creative Commons Attribution-Share Alike 3.0 Unported License’. viruSITE is a web-based relational database utilizing MySQL. Os x data recovery It operates on a Linux Slackware system under an Apache web server. R studio data recovery download Its web interface was developed using HTML/PHP. Data recovery western digital The viruSITE web pages make use of JavaScript/Ajax in order to enhance their dynamics and minimize data transfer. Top 5 data recovery software The proprietary genome browser phiGENOME, which is integrated into the viruSITE web interface framework, is built on Adobe Flash technology ( 13). Apart from PHP scripts handling database queries from users, various sequence analysis and visualization tools run in the viruSITE environment as well. Data recovery mac BLAST programs were implemented into the web interface to perform sequence similarity searches ( 14). Database website Circoletto, a visualization tool based on Circos, provides a graphical display of sequence similarity on full genome scale ( 15, 16) and also visual overview of sequence similarity between sequentially related viral genomes. Data recovery denver The MUSCLE program was employed for multiple sequence alignment and construction of phylogenetic trees ( 17). Data recovery galaxy s4 The jsPhyloSVG, JavaScript library, was used for visualising interactive vector-based phylogenetic trees via web interface ( 18). In addition to software running on a local server, BLAST programs are also executed on remote NCBI servers. R studio data recovery free full version For protein domain identification, Pfam searches are executed on remote servers of the Wellcome Trust Sanger Institute ( 19). Data recovery equipment A RESTful web service was implemented for programmatic interaction between local and remote servers. Database primary key viruSITE offers a simple way to identify sets of homologous genes and proteins as well as groups of related viral genomes. Database link oracle Sequence homology is determined by a local BLAST search. 7 data recovery key For gene and protein queries, the similarity is calculated on the fly, whereas for whole genome sequences it is pre-computed in a pairwise manner for each database release. Database manager salary BLAST searches are executed with default parameters, with the exception of those used to identify a virus’ relatives, where the threshold E-value of 1e−10 is used. viruSITE web interface. Database processing ( A) Keyword search—a search result for human herpes viruses. Database xcode ( B) Entry details page for human herpesvirus 5 (HHV-5). Database administrator salary ( C) Circoletto visualization of the sequence similarity between genomes related to HHV-5
. Data recovery iphone 4s ( D) HHV-5 genome … Keyword search provides a straightforward way to query the database. Fundamentals of database systems Search terms are looked up in conjunction with the following fields: Virus name, Taxonomy ID, Host name, Host group (terms used by the NCBI Viral Genome Resource), Genome type, Genome length and Genome RefSeq ID, Gene/protein name, Entrez Gene ID, Entrez Protein ID, UniProt ID, GO ID, GO term and Pfam ID. Database er diagram Up to three search terms/fields can be combined in order to refine the search. Data recovery tools linux When utilizing one of the ‘name’ fields, a wildcard character can be used as a suffix attached to a specific search term. Data recovery wizard for mac Official scientific names (e.g. Database etl Variola virus, Homo sapiens) and common names (e.g. Database lock smallpox virus, human) are equally accepted. Sequence search allows scanning a sequence of interest against all sequences of viral genomes and proteins in the database. Data recovery reviews Local BLAST search is employed to determine sequence similarity. In the Taxonomy Browser section, users can browse through the list of all viral species and higher taxonomic ranks deposited in the viruSITE database. Database d b Names of taxons are sorted alphabetically, and browsing through this list is facilitated by an Ajax auto-complete search script. Ads b database In addition, this section includes a drop-down taxonomic tree that enables hierarchical browsing throughout the viral taxonomy. The search/browse output is displayed in a tabular form and can be directly downloaded in a CSV format. Database denormalization Sequences can be downloaded in FASTA format. Pokemon y database The data in the table are sorted by clicking the column title. Data recovery icon Users can also change the number of displayed results per page. Fda 510 k database Selecting individual checkboxes located in the first column of the results table enables retrieval and analysis of the corresponding sequences (see the Retrieve and Analyse sections below). After clicking on an entry name, the entry details page is displayed. Google hacking database The virus details page contains information on virus nomenclature (official and alternative names), taxonomy, virus hosts, genome properties (type, length, number of segments, GC content, coding percentage, number of encoded genes, proteins and RNAs) and links to other online databases and literature references. Database concepts 6th edition pdf The gene/protein details page contains names, genomic position, length, molecular weight and pI, gene ontologies, protein domains and numerous links to other online databases and literature references. Data recovery utility Furthermore, each entry’s details page is linked to the graphical representation of a viral genome in the phiGENOME browser ( Genome Browser section), to the sequence display in a pop-up window as well as to the homology search and visualization. The Genome Browser section of the viruSITE web portal utilizes phiGENOME, the proprietary graphical genome browser. Data recovery from hard drive It provides a dynamic and interactive graphical representation of viral genomes. Database objects The genome browser consists of two interconnected components: (i) An Adobe Flash-based graphical applet, providing dynamic and interactive graphical display of genomes, and (ii) semi-graphical HTML-based output, providing detailed exploration of genome features on the sequence level. Data recovery raid 5 Both components are interconnected, thus any action performed in one of them (e.g. Database architect a change in zoom, position or gene selection) is instantly reflected in the other one. In the Retrieve section, users can view and download selected entries from the Search/Browse output table in a CSV format and sequences in FASTA format. Data recovery options Furthermore, complete collections of genome, gene and protein sequences deposited in the viruSITE database are available for retrieval on the Download page. There are numerous public databases which store information on viral genome sequences, genes and proteins, however none of them provides the same information and functionalities as viruSITE. Database jobs Most of databases are focused only on specific viruses (e.g. H2 database file influenza virus or HIV) or groups of viruses (e.g. R studio data recovery serial key hepatitis viruses or RNA viruses) ( 20), while viruSITE is a general resource for all virus taxa. Database query languages NCBI’s Viral Genome Resource is a complete repository for all reference viral genomes ( 4), and it provides curated sequence data and annotation for the complete viral genome sequences deposited in the RefSeq database. P d database However, the user interface offers limited options for searching this database. Database 101 For example, it is not possible to search protein entries directly. M power database VirGen (A Comprehensive Viral Genome Resource) was developed with the aim to serve as an annotated and curated database for all complete viral genomes, but this project has been idle for several years ( 21). Data recovery from external hard drive ViralZone is another comprehensive, visually attractive and virus-oriented information resource ( 7). Database join types While ViralZone contains examples from all known groups of viruses, there are relatively few reference species within each group (around 10% of the viruses covered by viruSITE). Section 8 database Users can easily retrieve and analyse protein sequences, but are limited to those which are deposited in UniProtKB/Swiss-Prot, and the information on viral genomes in ViralZone is covered only marginally. Icd 9 database There are also several predominantly single-purpose analysis tools available. Database xampp For example, Base-By-Base is available for the whole genome alignment ( 22) while ViroBLAST is available for the homology search among different datasets ( 23). Database administrator jobs However, some of the tools available in the past are not functional anymore, e.g. Data recovery joondalup GIB-V ( 24) or Alvira ( 25). The viruSITE database described here is an integrated database for general viral genomics. Database of genomic variants The database is currently holding entries for 5633 viruses, viroids and satellites. Database viewer The primary aim of viruSITE is to merge virus-oriented information from existing relevant sources and bring it to users in a concise and comprehensible form. H data recovery registration code free download A majority of this information is automatically extracted from the records found in reference databases (RefSeq, UniProtKB, Pfam, GO, ViralZone, NCBI Taxonomy and PubMed). Database hardware However, it is not merely a derivative of existing databases. Database roles The viruSITE content is manually and semi-automatically enhanced with the data that are not explicitly present (or are incomplete) in the records of reference databases, e.g. B tree database management system the names of genome segments (for viruses with a segmented genome and originated from provisional RefSeq records), the percentage of coding sequences in genomes or the isoelectric point for proteins. Database file The virus-to-host assignment has been improved by combining RefSeq and UniProt entries. Data recovery near me The unique data stored in the database are the mutual sequence similarity scores, defining groups of viral genomes which are related on the sequence level. Database job description These are calculated in a pairwise manner for each database release (see the ‘Database construction’ section for more details). Data recovery 94fbr viruSITE provides a user-friendly web interface coupled with powerful tools for searching, browsing, analysis and visualization. Database foreign key The search form provides versatile options in terms of retrieving complex information, e.g. Database as a service searching for viruses according to the host organism, taxonomical classification and genome properties. Iphone 6 data recovery Furthermore, users
can search for viral proteins according to the presence of a specific Pfam domain or on the basis of the gene ontology classification. Database google drive A combination of multiple search terms refines the search procedure and offers filtering of the data relevant from a biological point of view. Data recovery geek squad Particularly useful is the search based on sequence similarity which allows a quick finding of groups of homologous genes, proteins and related viral genomes. Database recovery pending All search results pages provide export features in different formats. Data recovery prices The graphics generated by the Circoletto/Circos bundle provides a schematic representation of sequence similarity at the level of entire viral genomes. Database sharding Another available visualization utility is phiGENOME—a genome browser providing a dynamic and responsive representation of a genome organization. Database keys with example A set of analysis tools for comparative genomics was incorporated into the user interface. Data recovery xfs All these features make viruSITE a unique and complex knowledge resource in the field of viral genomics. Database management systems 3rd edition viruSITE is hosted on the server of the Institute of Molecular Biology, Slovak Academy of Sciences and is freely accessible via the web portal virusite.org.

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