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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)

Abstract

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.

Keywords

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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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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