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. 1997 Aug 1;25(15):2960–2966. doi: 10.1093/nar/25.15.2960

Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution.

S L Chissoe 1, M A Marra 1, L Hillier 1, R Brinkman 1, R K Wilson 1, R H Waterston 1
PMCID: PMC146865  PMID: 9224593

Abstract

Representation of subcloned Caenorhabditis elegans and human DNA sequences in both M13 and pUC sequencing vectors was determined in the context of large scale genomic sequencing. In many cases, regions of subclone under-representation correlated with the occurrence of repeat sequences, and in some cases the under-representation was orientation specific. Factors which affected subclone representation included the nature and complexity of the repeat sequence, as well as the length of the repeat region. In some but not all cases, notable differences between the M13 and pUC subclone distributions existed. However, in all regions lacking one type of subclone (either M13 or pUC), an alternate subclone was identified in at least one orientation. This suggests that complementary use of M13 and pUC subclones would provide the most comprehensive subclone coverage of a given genomic sequence.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Brunak S., Engelbrecht J., Knudsen S. Prediction of human mRNA donor and acceptor sites from the DNA sequence. J Mol Biol. 1991 Jul 5;220(1):49–65. doi: 10.1016/0022-2836(91)90380-o. [DOI] [PubMed] [Google Scholar]
  3. Chen E. Y., Seeburg P. H. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA. 1985 Apr;4(2):165–170. doi: 10.1089/dna.1985.4.165. [DOI] [PubMed] [Google Scholar]
  4. Clarke L., Carbon J. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell. 1976 Sep;9(1):91–99. doi: 10.1016/0092-8674(76)90055-6. [DOI] [PubMed] [Google Scholar]
  5. Coulson A., Sulston J., Brenner S., Karn J. Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7821–7825. doi: 10.1073/pnas.83.20.7821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dear S., Staden R. A sequence assembly and editing program for efficient management of large projects. Nucleic Acids Res. 1991 Jul 25;19(14):3907–3911. doi: 10.1093/nar/19.14.3907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Fulton L. L., Wilson R. K. Variations on cycle sequencing. Biotechniques. 1994 Aug;17(2):298–301. [PubMed] [Google Scholar]
  8. Jurka J., Walichiewicz J., Milosavljevic A. Prototypic sequences for human repetitive DNA. J Mol Evol. 1992 Oct;35(4):286–291. doi: 10.1007/BF00161166. [DOI] [PubMed] [Google Scholar]
  9. Mardis E. R. High-throughput detergent extraction of M13 subclones for fluorescent DNA sequencing. Nucleic Acids Res. 1994 Jun 11;22(11):2173–2175. doi: 10.1093/nar/22.11.2173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Parsons J. D. Miropeats: graphical DNA sequence comparisons. Comput Appl Biosci. 1995 Dec;11(6):615–619. doi: 10.1093/bioinformatics/11.6.615. [DOI] [PubMed] [Google Scholar]
  11. Solovyev V. V., Salamov A. A., Lawrence C. B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Res. 1994 Dec 11;22(24):5156–5163. doi: 10.1093/nar/22.24.5156. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Sulston J., Du Z., Thomas K., Wilson R., Hillier L., Staden R., Halloran N., Green P., Thierry-Mieg J., Qiu L. The C. elegans genome sequencing project: a beginning. Nature. 1992 Mar 5;356(6364):37–41. doi: 10.1038/356037a0. [DOI] [PubMed] [Google Scholar]
  13. Thomas A., Skolnick M. H. A probabilistic model for detecting coding regions in DNA sequences. IMA J Math Appl Med Biol. 1994;11(3):149–160. doi: 10.1093/imammb/11.3.149. [DOI] [PubMed] [Google Scholar]
  14. Uberbacher E. C., Mural R. J. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11261–11265. doi: 10.1073/pnas.88.24.11261. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Wang M., Chen X. N., Shouse S., Manson J., Wu Q., Li R., Wrestler J., Noya D., Sun Z. G., Korenberg J. Construction and characterization of a human chromosome 2-specific BAC library. Genomics. 1994 Dec;24(3):527–534. doi: 10.1006/geno.1994.1662. [DOI] [PubMed] [Google Scholar]
  16. Wilson R., Ainscough R., Anderson K., Baynes C., Berks M., Bonfield J., Burton J., Connell M., Copsey T., Cooper J. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature. 1994 Mar 3;368(6466):32–38. doi: 10.1038/368032a0. [DOI] [PubMed] [Google Scholar]
  17. Wyman A. R., Wertman K. F. Host strains that alleviate underrepresentation of specific sequences: overview. Methods Enzymol. 1987;152:173–180. doi: 10.1016/0076-6879(87)52017-1. [DOI] [PubMed] [Google Scholar]

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