title: DNAGear--a free software for spa type identification in Staphylococcus aureus.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
authors.affiliation: Universidade do Algarve, DEEI-FCT, Faro, Portugal.
authors.forename: Faroq
authors.initials: F
authors.lastname: AL-Tam
authors.forename: Anne-Sophie
authors.initials: AS
authors.lastname: Brunel
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bouzinbi
authors.forename: Philippe
authors.initials: P
authors.lastname: Corne
authors.forename: Anne-Laure
authors.initials: AL
authors.lastname: Bañuls
authors.forename: Hamid Reza
authors.initials: HR
authors.lastname: Shahbazkia
mesh_terms: D000465:Algorithms; D015373:Bacterial Typing Techniques; D001483:Base Sequence; D004269:DNA, Bacterial; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid; D012984:Software; D013205:Staphylococcal Protein A / Q000145:classification / Q000235:genetics*; D013211:Staphylococcus aureus / Q000145:classification / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial; D013205:Staphylococcal Protein A