• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of narLink to Publisher's site
Nucleic Acids Res. Jun 15, 1998; 26(12): 3006–3012.
PMCID: PMC147651

Primer design for large scale sequencing.

Abstract

We have developed PRIDE, a primer design program that automatically designs primers in single contigs or whole sequencing projects to extend the already known sequence and to double strand single-stranded regions. The program is fully integrated into the Staden package (GAP4) and accessible with a graphical user interface. PRIDE uses a fuzzy logic-based system to calculate primer qualities. The computational performance of PRIDE is enhanced by using suffix trees to store the huge amount of data being produced. A test set of 110 sequencing primers and 11 PCR primer pairs has been designed on genomic templates, cDNAs and sequences containing repetitive elements to analyze PRIDE's success rate. The high performance of PRIDE, combined with its minimal requirement of user interaction and its fast algorithm, make this program useful for the large scale design of primers, especially in large sequencing projects.

Full Text

The Full Text of this article is available as a PDF (275K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Hunkapiller T, Kaiser RJ, Koop BF, Hood L. Large-scale and automated DNA sequence determination. Science. 1991 Oct 4;254(5028):59–67. [PubMed]
  • Messing J, Crea R, Seeburg PH. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. [PMC free article] [PubMed]
  • Messing J, Carlson J, Hagen G, Rubenstein I, Oleson A. Cloning and sequencing of the ribosomal RNA genes in maize: the 17S region. DNA. 1984;3(1):31–40. [PubMed]
  • Strauss EC, Kobori JA, Siu G, Hood LE. Specific-primer-directed DNA sequencing. Anal Biochem. 1986 Apr;154(1):353–360. [PubMed]
  • Kaiser RJ, MacKellar SL, Vinayak RS, Sanders JZ, Saavedra RA, Hood LE. Specific-primer-directed DNA sequencing using automated fluorescence detection. Nucleic Acids Res. 1989 Aug 11;17(15):6087–6102. [PMC free article] [PubMed]
  • Rosenblum BB, Lee LG, Spurgeon SL, Khan SH, Menchen SM, Heiner CR, Chen SM. New dye-labeled terminators for improved DNA sequencing patterns. Nucleic Acids Res. 1997 Nov 15;25(22):4500–4504. [PMC free article] [PubMed]
  • Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8794–8797. [PMC free article] [PubMed]
  • Ioannou PA, Amemiya CT, Garnes J, Kroisel PM, Shizuya H, Chen C, Batzer MA, de Jong PJ. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nat Genet. 1994 Jan;6(1):84–89. [PubMed]
  • Rychlik W, Rhoads RE. A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res. 1989 Nov 11;17(21):8543–8551. [PMC free article] [PubMed]
  • Hillier L, Green P. OSP: a computer program for choosing PCR and DNA sequencing primers. PCR Methods Appl. 1991 Nov;1(2):124–128. [PubMed]
  • Li P, Kupfer KC, Davies CJ, Burbee D, Evans GA, Garner HR. PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics. 1997 Mar 15;40(3):476–485. [PubMed]
  • Proutski V, Holmes EC. Primer Master: a new program for the design and analysis of PCR primers. Comput Appl Biosci. 1996 Jun;12(3):253–255. [PubMed]
  • Bonfield JK, Smith K f, Staden R. A new DNA sequence assembly program. Nucleic Acids Res. 1995 Dec 25;23(24):4992–4999. [PMC free article] [PubMed]
  • Sugimoto N, Nakano S, Yoneyama M, Honda K. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res. 1996 Nov 15;24(22):4501–4505. [PMC free article] [PubMed]
  • Breslauer KJ, Frank R, Blöcker H, Marky LA. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746–3750. [PMC free article] [PubMed]
  • Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. [PMC free article] [PubMed]
  • Martinez HM. An efficient method for finding repeats in molecular sequences. Nucleic Acids Res. 1983 Jul 11;11(13):4629–4634. [PMC free article] [PubMed]
  • Antao VP, Tinoco I., Jr Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res. 1992 Feb 25;20(4):819–824. [PMC free article] [PubMed]
  • Kwok S, Kellogg DE, McKinney N, Spasic D, Goda L, Levenson C, Sninsky JJ. Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Res. 1990 Feb 25;18(4):999–1005. [PMC free article] [PubMed]
  • Rivals E, Delgrange O, Delahaye JP, Dauchet M, Delorme MO, Hénaut A, Ollivier E. Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences. Comput Appl Biosci. 1997 Apr;13(2):131–136. [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles