DNA microarray technology and bioinformatic web services.

The pan-genomic microarray technique is used for environmental and/or clinical studies. Although microarray is an accurate and sharp diagnostic tool, the expertized bioinformaticians were able to minimize the outcome biases and maximize the flexibility and accuracy of the technique. The knowledge of bioinformatics plays a key role in association with probe designing and the utilization of correct probe sets and platforms. This technique is divided into two parts as dry lab (in silico studies) and wet lab (in vitro studies). Each part covers the other and are known as complementary divisions. In the case of microarray probe designing, a wide range of software, tools, and databases are necessary. Obviously, the application of right databases, software, and tools decreases the probable biases in the outcomes. Due to the importance of suitable probe designing, this article has focused its look onto a variety of online/offline databases, software, and tools.

[1]  Toshihisa Takagi,et al.  DNA Data Bank of Japan , 2016, Nucleic Acids Res..

[2]  Ivo Rendina,et al.  Silicon-Based Technology for Ligand-Receptor Molecular Identification , 2012 .

[3]  Payam Behzadi,et al.  The role of toll-like receptors (TLRs) in urinary tract infections (UTIs) , 2016, Central European journal of urology.

[4]  Henrik Bjørn Nielsen,et al.  OligoWiz 2.0—integrating sequence feature annotation into the design of microarray probes , 2005, Nucleic Acids Res..

[5]  Vincent Barra,et al.  PhylArray: phylogenetic probe design algorithm for microarray. , 2007, Bioinformatics.

[6]  G. López-Campos,et al.  DNA Microarrays: Principles and Technologies , 2012 .

[7]  Michael Wigler,et al.  PROBER: oligonucleotide FISH probe design software , 2006, Bioinform..

[8]  R. Ranjbar,et al.  Uropathogenic Escherichia coli virulence genes: invaluable approaches for designing DNA microarray probes , 2015, Central European journal of urology.

[9]  Erin Beck,et al.  The comprehensive microbial resource , 2000, Nucleic Acids Res..

[10]  Xiaowei Wang,et al.  Selection of Oligonucleotide Probes for Protein Coding Sequences , 2003, Bioinform..

[11]  Ikuo Uchiyama,et al.  MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity , 2009, Nucleic Acids Res..

[12]  S. Alavian,et al.  Nucleic Acid-Based Approaches for Detection of Viral Hepatitis , 2014, Jundishapur journal of microbiology.

[13]  E. Behzadi,et al.  Identification of 30‐kDa heat shock protein gene in Trichophyton  rubrum , 2009, Mycoses.

[14]  R. Ranjbar,et al.  IL-12 Family Cytokines: General Characteristics, Pathogenic Microorganisms, Receptors, and Signalling Pathways. , 2016, Acta microbiologica et immunologica Hungarica.

[15]  Harald Meier,et al.  46. ARB: A Software Environment for Sequence Data , 2011 .

[16]  S. Alavian,et al.  DNA microarray technology in HBV genotyping. , 2017, Minerva medica.

[17]  Eric C. Rouchka,et al.  MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays , 2005, BMC Bioinformatics.

[18]  Yun Zhang,et al.  ViPR: an open bioinformatics database and analysis resource for virology research , 2011, Nucleic Acids Res..

[19]  Steven Russell,et al.  MAMMOT - a set of tools for the design, management and visualization of genomic tiling arrays , 2006, Bioinform..

[20]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[21]  R. Ranjbar,et al.  Virulotyping of Shigella spp. isolated from pediatric patients in Tehran, Iran. , 2017, Acta microbiologica et immunologica Hungarica.

[22]  S. Yao,et al.  "Singapore Green": a new fluorescent dye for microarray and bioimaging applications. , 2009, Organic letters.

[23]  A. Bachmann,et al.  Reply from Authors re: [2_TD$DIFF]Jean-Nicolas [3_TD$DIFF]Cornu, [4_TD$DIFF]Stephan , 2015 .

[24]  A. Najafi,et al.  Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction , 2016, Central European journal of urology.

[25]  P. Behzadi Uropathogenic Escherichia coli and Fimbrial Adhesins Virulome , 2017, Urinary Tract Infection - The Result of the Strength of the Pathogen, or the Weakness of the Host.

[26]  Moo-Yeal Lee Overview of Microarray Bioprinting Technology , 2016 .

[27]  Raghavendra Hosur,et al.  ProbeSelect: selecting differentially expressed probes in transcriptional profile data , 2014, Bioinform..

[28]  A. Karami,et al.  Typing methods used in the molecular epidemiology of microbial pathogens: a how-to guide. , 2014, The new microbiologica.

[29]  David R. C. Hill,et al.  GoArrays: highly dynamic and efficient microarray probe design , 2005, Bioinform..

[30]  Li Tong,et al.  DaTo: an atlas of biological databases and tools , 2016, J. Integr. Bioinform..

[31]  Hans C. van Houwelingen,et al.  Microarray Data Analysis , 2004, Applied bioinformatics.

[32]  Xiaomin Ying,et al.  Mprobe 2.0 , 2006 .

[33]  Sophie Lemoine,et al.  An evaluation of custom microarray applications: the oligonucleotide design challenge , 2009, Nucleic acids research.

[34]  Adam M. Phillippy,et al.  Efficient oligonucleotide probe selection for pan-genomic tiling arrays , 2009, BMC Bioinformatics.

[35]  Paul C. H. Li Overview of Microarray Technology. , 2016, Methods in molecular biology.

[36]  Yuan Lin,et al.  IDT SciTools: a suite for analysis and design of nucleic acid oligomers , 2008, Nucleic Acids Res..

[37]  Payam Behzadi,et al.  Uropathogenic Escherichia coli: An Ideal Resource for DNA Microarray Probe Designing , 2017, IWBBIO.

[38]  M. Heller DNA microarray technology: devices, systems, and applications. , 2002, Annual review of biomedical engineering.

[39]  Hamid Mohamadi,et al.  BOND: Basic OligoNucleotide Design , 2013, BMC Bioinformatics.

[40]  Robert D. Finn,et al.  The European Bioinformatics Institute in 2016: Data growth and integration , 2015, Nucleic Acids Res..

[41]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[42]  R. Ranjbar,et al.  Advances in diagnosis and treatment of Helicobacter pylori infection. , 2017, Acta microbiologica et immunologica Hungarica.

[43]  Dong Xu,et al.  PRIMEGENSw3: A Web-Based Tool for High-Throughput Primer and Probe Design , 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine.

[44]  Siddharth Singh,et al.  AlleleID: a pathogen detection and identification system. , 2007, Methods in molecular biology.

[45]  Hui-Hsien Chou,et al.  Shared probe design and existing microarray reanalysis using PICKY , 2010, BMC Bioinformatics.

[46]  David R. C. Hill,et al.  HiSpOD: probe design for functional DNA microarrays , 2011, Bioinform..

[47]  Eric Peyretaillade,et al.  KASpOD - a web service for highly specific and explorative oligonucleotide design , 2012, Bioinform..

[48]  Ali Najafi,et al.  DNA Microarray for Rapid Detection and Identification of Food and Water Borne Bacteria: From Dry to Wet Lab , 2017, The open microbiology journal.

[49]  R. Cook-Deegan,et al.  Edwin Southern, DNA blotting, and microarray technology: A case study of the shifting role of patents in academic molecular biology , 2006, Genomics, society, and policy.

[50]  Rida Assaf,et al.  Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center , 2016, Nucleic Acids Res..

[51]  Chen-Zen Lo,et al.  UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/ genomic level , 2010, BMC Genomics.

[52]  Martin Dufva,et al.  Fabrication of high quality microarrays. , 2005, Biomolecular engineering.

[53]  Guy Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[54]  Ulf Landegren,et al.  ProbeMaker: an extensible framework for design of sets of oligonucleotide probes , 2005, BMC Bioinformatics.

[55]  R. Ranjbar,et al.  Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) Genotyping of Escherichia coli Strains Isolated from Different Animal Stool Specimens , 2016, Iranian journal of pathology.

[56]  Robert S. Matson Microarray Methods and Protocols , 2009 .

[57]  S. Petralia,et al.  A bridge-like solution for Universal Microarray applications , 2016 .

[58]  Jean-Marie Rouillard,et al.  OligoArray: genome-scale oligonucleotide design for microarrays , 2002, Bioinform..

[59]  R. Ranjbar,et al.  Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing , 2016, The open microbiology journal.

[60]  Fangfang Xia,et al.  The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) , 2013, Nucleic Acids Res..

[61]  Dorothea K. Thompson,et al.  DNA Microarray Technology , 2005 .

[62]  Moo-Yeal Lee,et al.  Microarray Bioprinting Technology Fundamentals and Practices , 2016 .

[63]  Antoine Margeot,et al.  Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments , 2010, Nucleic acids research.

[64]  G. López-Campos,et al.  Microarray Detection and Characterization of Bacterial Foodborne Pathogens , 2012 .

[65]  Jizhong Zhou,et al.  Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation , 2005, Nucleic acids research.