The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences
Download (696.12 kB)
-
Altmetric Citations
Gibbs, Mark; Fourment, Mathieu
Description
BACKGROUND: Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. RESULTS: The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as...[Show more]
dc.contributor.author | Gibbs, Mark | |
---|---|---|
dc.contributor.author | Fourment, Mathieu | |
dc.date.accessioned | 2009-04-23T02:18:11Z | |
dc.date.accessioned | 2010-12-20T06:06:13Z | |
dc.date.available | 2009-04-23T02:18:11Z | |
dc.date.available | 2010-12-20T06:06:13Z | |
dc.identifier.citation | BMC Bioinformatics 9.83 (2008) | |
dc.identifier.issn | 1471-2105 | |
dc.identifier.uri | http://hdl.handle.net/10440/131 | |
dc.identifier.uri | http://digitalcollections.anu.edu.au/handle/10440/131 | |
dc.description.abstract | BACKGROUND: Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. RESULTS: The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. CONCLUSION: VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically. | |
dc.format | 4 pages | |
dc.publisher | BioMed Central | |
dc.rights | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited | |
dc.source | BMC Bioinformatics | |
dc.source.uri | http://www.biomedcentral.com/content/pdf/1471-2105-9-83.pdf | |
dc.source.uri | http://www.biomedcentral.com/1471-2105/9/83 | |
dc.subject | Keywords: HTML pages; Java program; Large datasets; MySQL database; Partial sequences; RNA genome; Sequence database; Sequence lengths; Alignment; Computer software; Genes; Java programming language; Spreadsheets; Viruses; Database systems; amino acid sequence; art | |
dc.title | The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences | |
dc.type | Journal article | |
local.identifier.citationvolume | 9 | |
dcterms.dateAccepted | 2008-02-05 | |
dc.date.issued | 2008-02-05 | |
local.identifier.absfor | 060506 (50%), 080708 (50%) | |
local.identifier.ariespublication | u9511635xPUB273 | |
local.type.status | Published Version | |
local.contributor.affiliation | Gibbs, Mark, Faculty of Science, School of Botany and Zoology | |
local.contributor.affiliation | Fourment, Mathieu, Faculty of Science, School of Botany and Zoology | |
local.bibliographicCitation.issue | 83 | |
local.bibliographicCitation.startpage | 1 | |
local.bibliographicCitation.lastpage | 4 | |
local.identifier.doi | 10.1186/1471-2105-9-83 | |
dc.date.updated | 2015-12-09T09:23:29Z | |
local.identifier.scopusID | 2-s2.0-40549103796 | |
Collections | ANU Research Publications |
Download
File | Description | Size | Format | Image |
---|---|---|---|---|
Fourment_VirusBanker2008.pdf | 696.12 kB | Adobe PDF |
Items in Open Research are protected by copyright, with all rights reserved, unless otherwise indicated.
Updated: 17 November 2022/ Responsible Officer: University Librarian/ Page Contact: Library Systems & Web Coordinator