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Polypurine.polypyrimidine sequences in complete bacterial genomes: preference for polypurines in protein-coding
S Raghavan1, R Hariharan, S K Brahmachari
1Centre for Mathematical Modelling and Computer Simulation, Bangalore, India.
Gene
|March 18, 2000
Summary
Polypurine.polypyrimidine tracts show varied distribution across bacterial and archaeal genomes. Archaea have high abundance, while eubacteria have low abundance, with notable exceptions and strand biases observed.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Polypurine.polypyrimidine tracts are DNA sequence motifs.
- Their distribution and strand bias in microbial genomes are not fully understood.
Purpose of the Study:
- To analyze the presence and distribution of polypurine.polypyrimidine tracts in various microbial genomes.
- To investigate the strand bias of these sequences and potential explanations.
Main Methods:
- Bioinformatic analysis of genome sequences from selected bacteria and archaea.
- Comparative analysis of polypurine.polypyrimidine tract abundance and strand distribution.
Main Results:
- Significant variation in polypurine.polypyrimidine tract abundance was observed, with archaea showing high abundance and eubacteria low abundance.
- Mycobacterium tuberculosis and Aquifex aeolicus exhibited unique underrepresentation and overrepresentation, respectively.
- A preferential occurrence of polypurines on coding strands (strand bias) was noted, varying widely among species.
Conclusions:
- Genome-specific factors influence polypurine.polypyrimidine tract distribution and strand bias.
- The observed strand bias cannot be solely explained by GC-content, codon usage, or amino acid composition.