ALCOMFT-TR-02-61

Fariza Tahi, Manolo Gouy and Mireille Régnier
Automatic RNA secondary structure prediction with a comparative approach
INRIA. Work package 1. June 2002.

Abstract: This paper presents an algorithm that automatically predicts the common secondary structure of a set of aligned homologous RNA sequences. It is based on the comparative approach. Our algorithm searches in the target sequence for palindromes that have a high probability to define helices that are conserved in the test sequences. A recursive search of helices, starting from the likely ones, is implemented using the "divide and conquer" approach. The algorithm was run on ribosomal RNA sequences and recovered very efficiently their common secondary structures.

Postscript file: ALCOMFT-TR-02-61.ps.gz (126 kb).