@inproceedings{SiebertECCB02,
author = {Siebert, Sven},
title = {Multiple Local Sequence Structure Alignment of RNA
         Sequences},
booktitle = {European Conference on Computational Biology 2002},
year = {2002},
doi = {},
user = {siebert},
note = {Poster},
month = {October},
address = {Saarbrücken},
abstract = {We present a new method that finds and aligns local
            sequence structure segments in a set of unaligned
            RNA sequences of unknown structures. Recognizing
            secondary structural features allows us to find
            highly probable sequence structure segments with
            high similarities among them. There are a lot of
            multiple sequence programs which consider and handle
            primary sequences quite well. But they lack of
            finding and aligning structural features of RNA
            sequences. RNA sequences are often more conserved in
            their secondary structure than in their primary
            sequence. Sankoff was one of the first who proposed
            a dynamic programming algorithm that aligns a set of
            RNA sequences while predicting their common
            structures. The most promising approach is the use
            of stochastic context-free grammars (SCFG), which
            perform global alignments and find a covariance
            model. Covariance models work well in finding common
            structural constraints of whole RNA sequences but
            are not intended to find common local structure
            constraints. FOLDALIGN from G.D. Stormo is a program
            which considers sequence and structure motifs using
            nucleotide similarities and basepair maximization.}
}