title: BiDaS: a web-based Monte Carlo BioData Simulator based on sequence/feature characteristics.
abstract: BiDaS is a web-application that can generate massive Monte Carlo simulated sequence or numerical feature data sets (e.g. dinucleotide content, composition, transition, distribution properties) based on small user-provided data sets. BiDaS server enables users to analyze their data and generate large amounts of: (i) Simulated DNA/RNA and aminoacid (AA) sequences following practically identical sequence and/or extracted feature distributions with the original data. (ii) Simulated numerical features, presenting identical distributions, while preserving the exact 2D or 3D between-feature correlations observed in the original data sets. The server can project the provided sequences to multidimensional feature spaces based on: (i) 38 DNA/RNA features describing conformational and physicochemical nucleotide sequence features from the B-DNA-VIDEO database, (ii) 122 DNA/RNA features based on conformational and thermodynamic dinucleotide properties from the DiProDB database and (iii) Pseudo-aminoacid composition of the initial sequences. To the best of our knowledge, this is the first available web-server that allows users to generate vast numbers of biological data sets with realistic characteristics, while keeping between-feature associations. These data sets can be used for a wide variety of current biological problems, such as the in-depth study of gene, transcript, peptide and protein groups/families; the creation of large data sets from just a few available members and the strengthening of machine learning classifiers. All simulations use advanced Monte Carlo sampling techniques. The BiDaS web-application is available at http://bioserver-3.bioacademy.gr/Bioserver/BiDaS/.
authors.affiliation: Biomedical Informatics Unit, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 115 27 Athens, Greece.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Paraskevopoulou
authors.forename: Ioannis S
authors.initials: IS
authors.lastname: Vlachos
authors.forename: Emmanouil
authors.initials: E
authors.lastname: Athanasiadis
authors.forename: George
authors.initials: G
authors.lastname: Spyrou
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D020407:Internet; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D011506:Proteins / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D017421:Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA