We present a computational scheme to locally align a collection of RNA sequences using sequence and structure constraints. In addition, the method searches for the resulting alignments with the most significant common motifs, among all possible collections. The first part utilizes a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pair-wise comparisons. The algorithm finds the multiple alignments using a greedy approach and has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pair-wise alignments are optimized for both sequence and structure conservation. The choice of scoring system and the method of progressively constructing the final solution are important considerations that are discussed. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structures identical to published ones.

Original languageEnglish
Pages (from-to)3724-3732
Number of pages9
JournalNucleic acids research
Issue number18
StatePublished - Sep 15 1997


Dive into the research topics of 'Finding the most significant common sequence and structure motifs in a set of RNA sequences'. Together they form a unique fingerprint.

Cite this