Introduction

MOTIVATION: An apparent paradox in computational RNA structure prediction is that many methods, in advance, require a multiple alignment of a set of related sequences, when searching for a common structure between them. However, such a multiple alignment is hard to obtain even for few sequences with low sequence similarity without simultaneously folding and aligning them. Furthermore, it is of interest to conduct a multiple alignment of RNA sequence candidates found from searching as few as two genomic sequences. RESULTS: Here, based on the PMcomp program, we present a global multiple alignment program, foldalignM, which performs especially well on few sequences with low sequence similarity, and is comparable in performance with state of the art programs in general. In addition, it can cluster sequences based on sequence and structure similarity and output a multiple alignment for each cluster. Furthermore, preliminary results with local datasets indicate that the program is useful for post processing foldalign pairwise scans. AVAILABILITY: The program foldalignM is implemented in JAVA and is, along with some accompanying PERL scripts, available at http://foldalign.ku.dk/

Publications

  1. Multiple structural alignment and clustering of RNA sequences.
    Cite this
    Torarinsson E, Havgaard JH, Gorodkin J, 2007-04-01 - Bioinformatics (Oxford, England)
  2. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.
    Cite this
    Havgaard JH, Torarinsson E, Gorodkin J, 2007-10-01 - PLoS computational biology
  3. The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search.
    Cite this
    Havgaard JH, Lyngsø RB, Gorodkin J, 2005-07-01 - Nucleic acids research
  4. Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.
    Cite this
    Sundfeld D, Havgaard JH, de Melo AC, Gorodkin J, 2016-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Elfar Torarinsson
    Developer

  2. Jakob H Havgaard
    Developer

  3. Jan Gorodkin
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006595
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByJan Gorodkin