@article{Siebert:Backofen:MARNA_multi_align:2005,
author = {Siebert, Sven and Backofen, Rolf},
title = {{MARNA}: multiple alignment and consensus structure 
         prediction of {RNAs} based on sequence structure comparisons},
journal = {Bioinformatics},
year = {2005},
doi = {10.1093/bioinformatics/bti550},
volume = {21},
user = {siebert},
pmid = {15972285},
pages = {3352-9},
number = {16},
abstract = {MOTIVATION: Due to the importance of considering secondary 
            structures in aligning functional RNAs, several pairwise 
            sequence-structure alignment methods have been developed. 
            They use extended alignment scores that evaluate secondary 
            structure information in addition to sequence information. 
            However, two problems for the multiple alignment step 
            remain. First, how to combine pairwise sequence-structure 
            alignments into a multiple alignment and second, how to 
            generate secondary structure information for sequences whose 
            explicit structural information is missing. RESULTS: We 
            describe a novel approach for multiple alignment of RNAs 
            (MARNA) taking into consideration both the primary and the 
            secondary structures. It is based on pairwise 
            sequence-structure comparisons of RNAs. From these 
            sequence-structure alignments, libraries of weighted 
            alignment edges are generated. The weights reflect the 
            sequential and structural conservation. For sequences whose 
            secondary structures are missing, the libraries are 
            generated by sampling low energy conformations. The 
            libraries are then processed by the T-Coffee system, which 
            is a consistency based multiple alignment method. 
            Furthermore, we are able to extract a consensus-sequence and 
            -structure from a multiple alignment. We have successfully 
            tested MARNA on several datasets taken from the Rfam 
            database. AVAILABILITY: MARNA can be used online on our 
            webpage www.bio.inf.uni-jena.de/Software/MARNA/index.html }
}