DNASequenceGenerator

DNASequenceGenerator: A program for the construction of DNA sequences In DNA Computing and DNA nanotechnology the design of proper DNA sequences turned out to be an elementary problem. We here present a software program for the construction of sets (“pools”) of DNA sequences. The program can create DNA sequences to meet logical and physical parameters such as uniqueness, melting temperature and GC ratio as required by the user. It can create sequences de novo, complete sequences with gaps and allows import and recycling of sequences that are still in use. The program always creates sequences that are -- in terms of uniqueness, GC ratio and melting temperature -- “compatible” to those already in the pool, no matter whether those were added manually or created or completed by the program itself. The software comes with a GUI and a Sequence Wizard. In vitro tests of the program’s output were done by generating a set of oligomers designed for self-assembly. The software is available for download under http://LS11-www.cs.uni-dortmund.de/molcomp/Downloads/downloads.html.


References in zbMATH (referenced in 16 articles , 1 standard article )

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  1. Chaves-González, José M.; Vega-Rodríguez, Miguel A.: A multiobjective approach based on the behavior of fireflies to generate reliable DNA sequences for molecular computing (2014)
  2. Konstantinidis, Stavros; Santean, Nicolae: Computing maximal Kleene closures that are embeddable in a given subword-closed language (2013)
  3. Kari, Lila; Mahalingam, Kalpana: Watson-Crick palindromes in DNA computing (2010)
  4. Frank, Daniel N.: \itbarcrawland \itBARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing (2009) ioport
  5. Ibrahim, Zuwairie; Kurniawan, Tri Basuki; Khalid, Noor Khafifah; Sudin, Shahdan; Khalid, Marzuki: Implementation of an ant colony system for DNA sequence optimization (2009) ioport
  6. Zhang, Xuncai; Wang, Yanfeng; Cui, Guangzhao; Niu, Ying; Xu, Jin: Application of a novel IWO to the design of encoding sequences for DNA computing (2009) ioport
  7. Jonoska, Nataša; Mahalingam, Kalpana; Chen, Junghuei: Involution codes: with application to DNA coded languages (2005) ioport
  8. Garzon, Max H.; Deaton, Russell J.: Codeword design and information encoding in DNA ensembles (2004)
  9. Ibrahim, Zuwairie; Tsuboi, Yusei; Ono, Osamu; Khalid, Marzuki: A study on lower bound of direct proportional length-based DNA computing for shortest path problem (2004)
  10. Jonoska, Nataša: Trends in computing with DNA (2004) ioport
  11. Jonoska, Nataša; Mahalingam, Kalpana: Methods for constructing coded DNA languages (2004)
  12. Mauri, G.; Ferretti, C.: Word design for molecular computing: A survey (2004)
  13. Deaton, Russell; Chen, Junghuei; Bi, Hong; Rose, John A.: A software tool for generating non-crosshybridizing libraries of DNA oligonucleotides (2003)
  14. Feldkamp, Udo; Rauhe, Hilmar; Banzhaf, Wolfgang: Software tools for DNA sequence design (2003) ioport
  15. Kim, Dongmin; Shin, Soo-Yong; Lee, In-Hee; Zhang, Byoung-Tak: NACST/Seq: A sequence design system with multiobjective optimization (2003)
  16. Feldkamp, Udo; Saghafi, Sam; Banzhaf, Wolfgang; Rauhe, Hilmar: DNASequenceGenerator: A program for the construction of DNA sequences (2002)