OLIGO Primer Analysis Software

OLIGO Primer Analysis Software
OLIGO Primer Analysis Software
Developer(s) Molecular Biology Insights, Inc.
Stable release 7.54 / March 23, 2011
Operating system Windows, Macintosh
Platform Mac, PC
Type Bioinformatics
License commercial
Website http://oligo.net/

OLIGO Primer Analysis Software was the first publicly-available software for DNA primer design.[1][2] The first papers describing this software were published in 1989 and 1990,[3][4] and consecutive upgrades in the 1990-s and 2000-s, all have been cited together over 600 times in scientific journals and over 500 times in patents (according to Scopus). The program is a comprehensive real time PCR primer and probe search and analysis tool, and also does other tasks such as siRNA and molecular beacon searches, open reading frame and restriction enzyme analysis etc. It has been created and maintained by Wojciech Rychlik and Piotr Rychlik. The OLIGO has been reviewed several times in scientific journals, for the first time in 1991 in a review in Critical Reviews in Biochemistry and Molecular Biology,[5] and for its next upgrades (with OLIGO 7 being the latest one in 2011).[6][7][8][9]

Oligo Primer Analysis Software has been used in various scientific studies (as cited by examples of recent publications), among them for: real time PCR,[10] apoptosis studies,[11] antigen typing,[12] species identification,[13] studies on species evolution,[14] measuring mRNA expression levels,[15] oligonucleotide-based array hybridization studies,[16] degenerate primer studies,[17] microsatellite analysis,[18] DNA microarray detection,[19] inverse PCR,[20] genome walking,[21] nucleotide polymorphisms studies,[22] detection of microorganisms or viruses,[23] genotyping,[24] cloning,[25] vector (gene) construction,[26] genome sequencing,[27] detection of mutants or intraspecific variability,[28] genetic disease studies,[29] siRNA and gene silencing,[30] FISH analysis (single cell expression study),[31] scorpion probes,[32] and development of new DNA amplification methods.[33]

References

  1. ^ John SantaLucia, Jr. (2007) Basic Principles and Software for PCR Primer Design: Physical Principles and Visual-OMP Software for Optimal PCR Design, in Methods in Molecular Biology Vol. 402: PCR Primer Design; Ed. A. Yuryev; Humana Press Inc., Totowa, NJ. pp. 3-33.
  2. ^ John D. Offerman, Wojciech Rychlik (2003) Oligo Primer Analysis Software in Introduction to bioinformatics: a theoretical and practical approach. Ed. Stephen A. Krawetz and David D. Womble; Humana Press Inc., Totowa, NJ. pp. 345-361.
  3. ^ Wojciech Rychlik and Robert E. Rhoads (1989) A Computer Program for Choosing Optimal Oligonucleotides for Filter Hybridization, Sequencing and in vitro Amplification of DNA; Nucleic Acids Research 17, 8543-8551.
  4. ^ Wojciech Rychlik, William J. Spencer, and Robert E. Rhoads (1990) Optimization of the Annealing Temperature for DNA Amplification in Vitro; Nucleic Acids Res. 18, 6409-6412.
  5. ^ Bej AK, Mahbubani MH, and Atlas RM (1991). "Amplification of Nucleic Acids by Polymerase Chain Reaction (PCR) and Other Methods and Their Applications". Crit. Rev. Biochem. Mol. Biol. 26 (3-4): 301–34. doi:10.3109/10409239109114071. PMID 1718663. 
  6. ^ Kamel A. Abd-Elsalam (2003) Bioinformatic Tools and Guideline for PCR Primer Design; African Journal of Biotechnology 2, 91-95.
  7. ^ Wojciech Rychlik (2007). "OLIGO 7 Primer Analysis Software". Methods Mol. Biol. 402: 35–60. doi:10.1007/978-1-59745-528-2_2. PMID 17951789. 
  8. ^ www.biocompare.com/review/682/Oligo-Primer-Analysis-Software-From-Molecular-Biology-Insights.html
  9. ^ Wojciech Rychlik (1993) Selection of Primers for Polymerase Chain Reaction, in Methods in Molecular Biology Vol. 15: PCR Protocols: Current Methods and Applications; Ed. B.A. White; Humana Press Inc., Totowa, NJ. pp. 31-40.
  10. ^ Arneth Borros (2009) Following Ionic Activity by Electrochemistry During the Polymerase Chain Reaction; Analytical Biochemistry 385, 26-33.
  11. ^ Arabinda Das, Naren L. Banik, and Swapan K. Ray (2008) Modulatory Effects of Acetazolomide and Dexamethasone on Temozolomide Mediated Apoptosis in Human Glioblastoma T98G and U87MG Cells; Cancer Investigation 26, 352 - 358.
  12. ^ Sarah H. Haddock, Christine Quartararo, Patrick Cooley, and Dat D. Dao (2002) Low-Resolution Typing of HLA-DQA1 Using DNA Microarray, Methods in Molecular Biology 170, 201-210.
  13. ^ Marco Severgnini, Paola Cremonesi, Clarissa Consolandi, Giada Caredda, Gianluca De Bellis and Bianca Castiglioni (2009) ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design; Nucleic Acids Research 37 (16), e109.
  14. ^ Arhat Abzhanov (2009). "Darwin’s Finches: Analysis of Beak Morphological Changes During Evolution". Cold Spring Harbor Protocols. Emerging model organisms 1 (3): 481–500. doi:10.1101/pdb.emo119. 
  15. ^ Canhui Liu, Chitra Chauhan, Charles R. Katholi, and Thomas R. Unnasch (2009) The splice leader addition domain represents an essential conserved motif for heterologous gene expression in B. malayi; Molecular & Biochemical Parasitology 166, 15–21.
  16. ^ Daryl A. Scott, Merel Klaassens, Ashley M. Holder, Kevin P. Lally, Caraciolo J. Fernandes, Robert-Jan Galjaard, Dick Tibboel, Annelies de Klein, and Brendan Lee (2007) Genome-Wide Oligonucleotide-Based Array Comparative Genome Hybridization Analysis of Non-Isolated Congenital Diaphragmatic Hernia; Human Molecular Genetics. 16, 424-430.
  17. ^ Omar J. Jabado, Gustavo Palacios, Vishal Kapoor, Jeffrey Hui, Neil Renwick, Zhai Junhui, Thomas Briese, and W. Ian Lipkin (2006) Greene SCPrimer: a Rapid Comprehensive Tool for Designing Degenerate Primers from Multiple Sequence Alignments; Nucleic Acids Research. 34, 6605-6611.
  18. ^ Alberto Arias, Ruth Freire, Josefina Méndez, and Ana Insua (2010) Isolation and characterization of microsatellite markers in the queen scallop Aequipecten opercularis and their application to a population genetic study; Aquatic Living Resources 23, 199 - 207.
  19. ^ Frédérique Bidard, Sandrine Imbeaud, Nancie Reymond, Olivier Lespinet, Philippe Silar, Corinne Clavé, Hervé Delacroix, Véronique Berteaux-Lecellier and Robert Debuchy (2010) A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina; BMC Research Notes 3, 171.
  20. ^ Kazutaka Yamada, Takeshi Terahara, Shinya Kurata, Toyokazu Yokomaku, Satoshi Tsuneda, and Shigeaki Harayama (2008) Retrieval of Entire Genes from Environmental DNA by Inverse PCR with Pre-Amplification of Target Genes Using Primers Containing Locked Nucleic Acids; Environmental Microbiology 10, 978 - 987.
  21. ^ Tokuji Tsuchiya, Nanako Kameya, and Ikuo Nakamura (2009). "Straight Walk: A modified method of ligation-mediated genome walking for plant species with large genomes". Analytical Biochemistry 388 (1): 158–160. doi:10.1016/j.ab.2009.02.002. PMID 19454221. 
  22. ^ O. A. Gra, A. S. Glotov, Zh. M. Kozhekbayeva, O. V. Makarova, and T. V. Nasedkina (2008) Genetic Polymorphism of GST, NAT2 , and MTRR and Susceptibility to Childhood Acute Leukemia; Molecular Biology 42, 187-197.
  23. ^ T. Wei, G. Lu, and G. R. G. Clover (2009) A Multiplex RT-PCR for the Detection of Potato Yellow Vein Virus, Tobacco Rattle Virus and Tomato Infectious Chlorosis Virus in Potato with a Plant Internal Amplification Control; Plant Pathology 58, 203-209.
  24. ^ Kristel Van Laethema, Yoeri Schrootena, Kris Covensa, Nathalie Dekeersmaekera, Paul De Munterc, Eric Van Wijngaerdenc, Marc Van Ransta, and Anne-Mieke Vandamme (2008) A Genotypic Assay for the Amplification and Sequencing of Integrase from Diverse HIV-1 Group M Subtypes; Journal of Virological Methods 153, 176-181.
  25. ^ Elena K. Khlestkina, Uttam Kumar, and Marion S. Röder (2010) Ent-kaurenoic acid oxidase genes in wheat; Molecular Breeding 25, 251–258.
  26. ^ Guozheng Conga, Jianhua Zhoua, Shandian Gaoa, Junzheng Dua, Junjun Shaoa, Tong Lina, Huiyun Chang, and Qingge Xie (2008) Construction of Recombinant Retroviral Vector Carrying Lab Gene of Foot-and-Mouth Disease Virus and Its Expression in Bovine Kidney (MDBK) Cells; Chinese Journal of Biotechnology 24, 740-745.
  27. ^ Lei Wei, Xiaobing Wu, and Zhigang Jiang (2009) The complete mitochondrial genome structure of snow leopard Panthera uncia; Molecular Biology Reports 36, 871–878.
  28. ^ David S. Perlin, Sergey Balashov, and Steven Park (2008) Multiplex Detection of Mutations; Methods in Molecular Biology 429, 23-31.
  29. ^ Michele Salemi, Corrado Romano, Concetta Barone, Francesco Cali, Filippo Caraci, Carmelo Romano, Cataldo Scavuzzo, Francesco Scillato, Maria Grazia Salluzzo, Maria Piccione, Manuela Martines, Giovanni Corsello, Ferdinando Nicoletti, and Paolo Bosco (2009) SPANX-B and SPANX-C (Xq27 region) gene dosage analysis in Down’s syndrome subjects with undescended testes; Journal of Genetics 88, 93-97.
  30. ^ Anastasia Khvorova, Angela Reynolds, and Sumedha D. Jayasena (2003) Functional siRNA and miRNAs Exhibit Strand Bias; Cell, 115, 209-216.
  31. ^ Rossanna C. Pezo, Saumil J. Gandhi, L. Andrew Shirley, Richard G. Pestell, Leonard H. Augenlicht, and Robert H. Singer (2008) Single-Cell Transcription Site Activation Predicts Chemotherapy Response in Human Colorectal Tumors; Cancer Research 68, 4977-4982.
  32. ^ Rachael Carters, Jennifer Ferguson, Rupert Gaut, Paul Ravetto, Nicola Thelwell, and David Whitcombe (2008) Design and Use of Scorpions Fluorescent Signaling Molecules; Methods in Molecular Biology 429, 99-115.
  33. ^ Chunsun Zhang and Da Xing (2010) Microfluidic gradient PCR (MG-PCR): a new method for microfluidic DNA amplification; Biomedical Microdevices 12, 1-12.

Other Primer Design Software

For more information about primer analysis freeware, please see the Primer entry.


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