title: A web-oriented software for the optimization of pooled experiments in NGS for detection of rare mutations.
abstract: BACKGROUND
  The cost per patient of next generation sequencing for detection of rare mutations may be significantly reduced using pooled experiments. Recently, some techniques have been proposed for the planning of pooled experiments and for the optimal allocation of patients into pools. However, the lack of a user friendly resource for planning the design of pooled experiments forces the scientists to do frequent, complex and long computations.
  
  
  RESULTS
  OPENDoRM is a powerful collection of novel mathematical algorithms usable via an intuitive graphical user interface. It enables researchers to speed up the planning of their routine experiments, as well as, to support scientists without specific bioinformatics expertises. Users can automatically carry out analysis in terms of costs associated with the optimal allocation of patients in pools. They are also able to choose between three distinct pooling mathematical methods, each of which also suggests the optimal configuration for the submitted experiment. Importantly, in order to keep track of the performed experiments, users can save and export the results of their experiments in standard tabular and charts contents.
  
  
  CONCLUSIONS
  OPENDoRM is a freely available web-oriented application for the planning of pooled NGS experiments, available at: http://www-labgtp.na.icar.cnr.it/OPENDoRM. Its easy and intuitive graphical user interface enables researchers to plan theirs experiments using novel algorithms, and to interactively visualize the results.
authors.affiliation: LabGTP (Laboratory of Genomics, Transcriptomics and Proteomics), Institute for High Performance Computing and Networking (ICAR), National Research Council (CNR), Via Pietro Castellino 111, 80131, Naples, Campania, Italy. daniela.evangelista@na.icar.cnr.it.
authors.forename: Daniela
authors.initials: D
authors.lastname: Evangelista
authors.affiliation: Department of Computer Science, University of Naples Parthenope, Via Amm. F. Acton, 80133, Naples, Italy. a.zuccaro@studenti.uniparthenope.it.
authors.forename: Antonio
authors.initials: A
authors.lastname: Zuccaro
authors.affiliation: Institute of Mathematics and Informatics, Vilnius University, Akademijos 4, 08663, Vilnius, Lithuania. lancinskas@mii.vu.lt.
authors.forename: Algirdas
authors.initials: A
authors.lastname: Lančinskas
authors.affiliation: Institute of Mathematics and Informatics, Vilnius University, Akademijos 4, 08663, Vilnius, Lithuania. julius.zilinskas@mii.vu.lt.
authors.forename: Julius
authors.initials: J
authors.lastname: Žilinskas
authors.affiliation: LabGTP (Laboratory of Genomics, Transcriptomics and Proteomics), Institute for High Performance Computing and Networking (ICAR), National Research Council (CNR), Via Pietro Castellino 111, 80131, Naples, Campania, Italy. mario.guarracino@cnr.it.
authors.forename: Mario R
authors.initials: MR
authors.lastname: Guarracino
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D004247:DNA / Q000032:analysis* / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods / Q000706:statistics & numerical data*; D006801:Humans; D020407:Internet; D009154:Mutation; D014584:User-Computer Interface
chemical_list: D004247:DNA