Help information


Table of Contents

  1. Contact
  2. Terms used in OligoSpawn
  3. Reference


Contact

OligoSpawn was developed by Jie Zheng when he was a Ph.D. student in Computer Science at UCR (now a research associate at NCBI/NLM/NIH), Dr. Timothy J. Close (Professor, Botany and Plant Sciences), Dr. Stefano Lonardi (Associate Professor, Computer Science), and Dr. Tao Jiang (Professor, Computer Science) at the University of California, Riverside (UCR). Please forward any inquiry to email "zhengj at ncbi dot nlm dot nih dot gov").


Terms used in OligoSpawn

  1. EST (Expressed sequence tags): Partial sequences of expressed genes, usually 200-700 bases long, which are generated by sequencing from one or both ends of cDNAs.

  2. Color: Number of distinct unigenes to which an oligo can hybridize.

  3. Oligo (oligonucleotides): A short chain of nucleotides, typically 20-50 bases, that contains special patterns.

  4. Unique oligo: An oligo that appears (exactly) in one unigene, but does not appear (exactly or approximately) on any other unigene.

  5. Popular oligo: An oligo that appears (exactly or approximately) in as many unigenes as possible.

  6. Overgo (overlapping oligonuceotide): Overgo probes are produced using two oligos that are comple-mentary to each other and anneal to form a double-stranded region. For 36-mer overgo probes, two 22-mers create the initial template for DNA synthesis, overlapping in 8 bps, leading to the production of a labeled probe.

  7. Core: A subsequence of a popular oligo that are guaranteed to perfect-match a unigene. One oligo could have multiple different cores, depending on which unigenes it matches with.

  8. Seed: A subsequence of a unique oligo that matches a unigenes with at most one mismatch. One oligo could have multiple different seeds, depending on which unigene it matches.

  9. Occurrence of oligos: The number of different locations on unigenes that an oligo occurs.

  10. Unigene: The unigene set for an organism should contain one consensus sequence representing each assembly of ESTs, and each unassembled (singleton) EST sequence.

  11. GC content: The percentage of nitrogenous bases on a DNA molecule which are either guanine or cytosine (from a possibility of four different ones, also including adenine and thymine).

  12. Melting temperature: The midpoint in the change in optical properties (absorbance, rotation) of a structured polymer (e.g., DNA) with increasing temperature.


References

J. Zheng, J. Svensson, T. Close, T. Jiang, S. Lonardi, "OligoSpawn: a software tool for the design of overgo probes from large unigene databases", accepted by BMC Bioinformatics, 2005.

J. Zheng, T. Close, T. Jiang, S. Lonardi, "Efficient Selection of Unique and Popular Oligos for Large unigene Databases", Bioinformatics,, Vol.20, no.13, pp.2101-2112, 2004.

J. Zheng, T. Close, T. Jiang, S. Lonardi, "Efficient Selection of Unique and Popular Oligos for Large unigene Databases", Proceedings of Symposium on Combinatorial Pattern Matching (CPM'03), pp.273-283, LNCS 2676, Morelia, Mexico, 2003.