Search for Evolution-Related-Oligonucleotides and Conservative Words in rRNA Sequences

We describe a method for finding ungapped conserved words in rRNA sequences that is effective, utilizes evolutionary information and does not depend on multiple sequence alignment. Evolutionary distance (called ndistance) between a pair of 16S or 18S rRNA sequences is defined in terms of the difference in the two sets of frequencies of occurrence of oligonucleotides n bases long (n-mers) given by the sequences. These n-distances are used to reconstruct phylogenetic trees for 35 representative organisms from all three kingdoms. The quality of the tree generally improves with increasing n and reaches a plateau of best fit at n=7 or 8. Hence the 7-mer or 8-mer (oligonucleotide of 7 or 8 bases) frequencies provide a basis to describe rRNA evolution. Based on the analysis of the contribution of a particular 7-mers to 7-distances, a set of 612 7-mers (called evolution-related-oligonucleotides, EROs) that are critical to the topology of the best phylogenetic tree are identified. Expanding fr...

• Type: Conference
• Year: 2003
• Where: CSB
• Authors: Liaofu Luo, Li-Ching Hsieh, Fengmin Ji, Mengwen Jia, H. C. Lee
• Keywords: 18S RRNA Sequences, CSB 2003, Phylogenetic Tree, RRNA Sequences