Nucleotide frequency map: A new technique for pictorial representation of dinucleotide frequencies

In this communication, a method of presentation of dinucleotide frequencies in the form of a contour diagram (map), designated as dinucleotide frequency map (DNFM), has been used for the first time to analyse the compositional bias of different nucleic acid sequences. Such maps provide a method of v...

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Bibliographic Details
Published in:Current science (Bangalore) 1996-07, Vol.71 (1), p.50-53
Main Authors: Pan, Archana, Basu, Soumalee, Dutta, Chitra, Burma, Debi Prasad, Mukherjee, Ranjana
Format: Article
Language:English
Subjects:
Base composition
Genomes
Music analysis
Nucleic acids
Nucleotide sequences
Nucleotides
Open reading frames
RESEARCH COMMUNICATIONS
Ribosomal DNA
rRNA genes
Vertices
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Summary:In this communication, a method of presentation of dinucleotide frequencies in the form of a contour diagram (map), designated as dinucleotide frequency map (DNFM), has been used for the first time to analyse the compositional bias of different nucleic acid sequences. Such maps provide a method of visualization of the nucleotide usage at a glance and allow simultaneous representation and comparative analysis of multiple sequences of different origins. Using the technique of DNFMs, it has been shown that the dinucleotide frequency distribution profile of any nucleotide sequence often exhibits distinct statistical bias, which is not predictable from the knowledge of its base composition. Analysis of bacterial rDNA operons showed that 16S and 23S rRNA genes of such species, in general, follow similar dinucleotide patterns, which are different from those of the intervening regions. The technique of DNFM has also been applied to analyse the compositional heterogeneity of the genomic sequence of the bacteriophage lambda to show that the dinucleotide frequencies vary along the phage genome depending on the distribution of open reading frames.
ISSN:0011-3891