Relation of Residues in the Variable Region of 16S rDNA Sequences and Their Relevance to Genus-Specificity

  • Maciej Liśkiewicz
  • Hemant J. Purohit
  • Dhananjay V. Raje
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3240)


It has been observed that the short nucleotide sequences in a variable region, representing species level diversity in a set of 16S rDNA sequences carries the genus specific signature. In this study our aim is to assess the relationship of residues at different positions and thereby obtain consensus patterns using different statistical tools. If such patterns are found genus-specific then it would facilitate in designing hybridization arrays to target even unexplored species of the same genus in complex samples such as environmental DNA.

For obtaining consensus pattern from a set of aligned sequences, four different methods were used on five bacterial genera. The patterns were tested for genus-specificity using BLAST. In two out of the five genera, the consensus pattern was highly genus-specific and was identified as a signature pattern representing the genera. In other genera, although the sample sub-sequences had the edge on the consensus pattern with respect to genus-specificity, there was not much difference between the consensus pattern and the signature pattern of these genera.


Mutual Information Variable Region Query Sequence Bacterial Genus Signature Pattern 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Amann, R.I., Ludwig, W., Schleifer, K.-H.: Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169 (1995)Google Scholar
  2. 2.
    Chen, J., Banks, D., Jarret, R.L., Chang, C.J., Smith, B.J.: Use of 16S rDNA sequences as signature characters to identify Xylella fastidiosa. Curr Microbiol. 40, 29–33 (2000)CrossRefGoogle Scholar
  3. 3.
    Demarta, A., Tonolla, A.-P., Caminada, N., Ruggeri, R., Peduzzi, R.: Signature region within 16S rDNA sequences of Aeromonas popofii. FEMS Microbiol. Letts 172, 239–246 (1999)CrossRefGoogle Scholar
  4. 4.
    Fox, G.E., Stackebrandt, E., Hespel, R.B., Gibson, J., Maniloff, J., Dyer, T.A., Wolfe, R.S., Balch, W.E., Tanner, R.S., Magrum, L.J., Zablen, L.B., Blakemore, R., Gupta, R., Bonen, L., Lewis, B.J., Stahl, D.A., Luchrsen, K.R., Chen, K.N., Woese, C.R.: The phylogeny of prokaryotes. Science 209, 457–463 (1980)CrossRefGoogle Scholar
  5. 5.
    Frances, M., Litman, A.: On covering problems of codes. Theory of Comput. Syst. 30(2), 113–119 (1997)zbMATHMathSciNetGoogle Scholar
  6. 6.
    Gupta, S., Kapoor, V.: Fundamentals of Mathematical Statistics. Sultan Chand & Sons, New Delhi (1986)Google Scholar
  7. 7.
    Hertz, G., Stormo, G.: Identifying DNA and Protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15, 563–577 (1999)CrossRefGoogle Scholar
  8. 8.
    Kataoka, M., Ueda, K., Takuji, K., Tatsuji, S., Toshiomi, Y.: Application of the variable region in 16S rDNA to create an index for rapid species identification in the genus Streptomyces FEMS Microbiol. Letts. 151, 249–255 (1997)Google Scholar
  9. 9.
    Lanctot, J., Li, M., Ma, B., Wang, S., Zhang, L.: Distinguishing string selection problems. In: Proc. 10th ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 633–642. ACM Press, New York (1999)Google Scholar
  10. 10.
    Monstein, H.J., Kihlostrom, E., Tiveljung, A.: Detection and identification of bacteria using in-house broad range 16S rDNA PCR amplification and genus-specific hybridization probes, located within variable regions of 16S rRNA genes. APMIS 104(6), 451–458 (1996)CrossRefGoogle Scholar
  11. 11.
    Moron, R., Gonzalez, I., Genilloud, O.: New genus-specific primers for the PCR identification of members of the genera Pseudonocardia and Saccharopolyspora. Int. J. Syst. Bacteriol. 49, 142–162 (1999)CrossRefGoogle Scholar
  12. 12.
    Purohit, H.J., Raje, D.V., Kapley, A.: Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences. BMC Bioinformatics 4, 19 (2003)CrossRefGoogle Scholar
  13. 13.
    Raje, D.V., Purohit, H.J., Singh, R.S.: Distinguishing features of 16S rDNA gene for five dominating bacterial genus observed in bioremediation. Journal of Computational Biology 9(6), 819–829 (2002)CrossRefGoogle Scholar
  14. 14.
    Shannon, C.: A mathematical theory of communication. The Bell System Techn. Journal 27, 379–423 (1948)zbMATHMathSciNetGoogle Scholar
  15. 15.
    Steuer, R., Kurths, J., Daub, C.O., Weise, J., Selbig, J.: The mutual information: Detecting and evaluating dependencies between variables. Bioinformatics 18, S231– S240 (2002)Google Scholar
  16. 16.
    Zhang, Z., Willson, R.C., Fox, G.: Identification of characteristic oligonulceotides in the bacterial 16S ribosomal RNA sequence dataset. Bioinformatics 18, 244–250 (2002)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Maciej Liśkiewicz
    • 1
  • Hemant J. Purohit
    • 2
  • Dhananjay V. Raje
    • 2
  1. 1.Institut für Theoretische InformatikUniversität zu LübeckLübeckGermany
  2. 2.Environmental Modeling and Genomics DivisionNational Environmental Engineering Research Institute, Nehru MargNagpurIndia

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