dc.contributor.author	Al-Tam, Faroq
dc.contributor.author	Brunel, Anne-Sophie
dc.contributor.author	Bouzinbi, Nicolas
dc.contributor.author	Corne, Philippe
dc.contributor.author	Bañuls, Anne-Laure
dc.contributor.author	Shahbazkia, Hamid Reza
dc.date.accessioned	2013-05-06T13:40:57Z
dc.date.available	2013-05-06T13:40:57Z
dc.date.issued	2012-11-19
dc.date.updated	2013-03-21T08:06:43Z
dc.description.abstract	Staphylococcus aureus is both human commensal and an important human pathogen, responsible for community-acquired and nosocomial infections ranging from superficial wound infections to invasive infections, such as osteomyelitis, bacteremia and endocarditis, pneumonia or toxin shock syndrome with a mortality rate up to 40%. S. aureus reveals a high genetic polymorphism and detecting the genotypes is extremely useful to manage and prevent possible outbreaks and to understand the route of infection. One of current and expanded typing method is based on the X region of the spa gene composed of a succession of repeats of 21 to 27 bp. More than 10000 types are known. Extracting the repeats is impossible by hand and needs a dedicated software. Unfortunately the only software on the market is a commercial program from Ridom. Findings This article presents DNAGear, a free and open source software with a user friendly interface written all in Java on top of NetBeans Platform to perform spa typing, detecting new repeats and new spa types and synchronizing automatically the files with the open access database. The installation is easy and the application is platform independent. In fact, the SPA identification is a formal regular expression matching problem and the results are 100% exact. As the program is using Java embedded modules written over string manipulation of well established algorithms, the exactitude of the solution is perfectly established. Conclusions DNAGear is able to identify the types of the S. aureus sequences and detect both new types and repeats. Comparing to manual processing, which is time consuming and error prone, this application saves a lot of time and effort and gives very reliable results. Additionally, the users do not need to prepare the forward-reverse sequences manually, or even by using additional tools. They can simply create them in DNAGear and perform the typing task. In short, researchers who do not have commercial software will benefit a lot from this application.	por
dc.description.version	info:eu-repo/semantics/publishedVersion
dc.identifier.citation	BMC Research Notes. 2012 Nov 19;5(1):642	por
dc.identifier.doi	10.1186/1756-0500-5-642
dc.identifier.uri	http://hdl.handle.net/10400.1/2686
dc.language.iso	eng	por
dc.peerreviewed	yes	por
dc.publisher	BioMed Central	por
dc.relation.publisherversion	http://www.biomedcentral.com/1756-0500/5/642	por
dc.rights.holder	Faroq AL-Tam et al.; licensee BioMed Central Ltd.
dc.rights.uri	http://creativecommons.org/licenses/by/2.0
dc.title	DNAGear: a free software for spa type identification in Staphylococcus aureus	por
dc.type	journal article
dspace.entity.type	Publication
oaire.citation.issue	1	por
oaire.citation.title	BMC Research Notes	por
oaire.citation.volume	5	por
person.familyName	Al-Tam
person.familyName	Shahbazkia
person.givenName	Faroq
person.givenName	Hamid Reza
person.identifier	R-00G-A33
person.identifier.ciencia-id	2515-AFE3-525F
person.identifier.ciencia-id	5D12-F388-568E
person.identifier.orcid	0000-0001-9718-2039
person.identifier.orcid	0000-0002-5661-0612
person.identifier.rid	K-7031-2016
person.identifier.scopus-author-id	55246034700
person.identifier.scopus-author-id	22735637800
rcaap.rights	openAccess	por
rcaap.type	article	por
relation.isAuthorOfPublication	15ac97f4-a867-462d-9fc6-0a47bb2919d3
relation.isAuthorOfPublication	11ed60f1-defe-4034-9203-633a116cf217
relation.isAuthorOfPublication.latestForDiscovery	15ac97f4-a867-462d-9fc6-0a47bb2919d3

DNAGear: a free software for spa type identification in Staphylococcus aureus

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