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PMID: 15980555 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search.

Nucleic acids research ·Vol. 33 ·No. Web Server issue ·2005-07-01 ·Pages W650-3

Havgaard JH, Lyngsø RB, Gorodkin J

Abstract

Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of foldalign. The server can be used to scan two sequences for a common structural RNA motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. The web server can be accessed at http://foldalign.kvl.dk.

MeSH Terms
Algorithms Computer Graphics Internet Nucleic Acid Conformation RNA/chemistry Sequence Alignment/methods Sequence Analysis, RNA/methods Software User-Computer Interface
Chemicals
RNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Havgaard Jakob H
Center for Bioinformatics and Division of Genetics, IBHV, The Royal Veterinary and Agricultural University Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.
Lyngsø Rune B
Gorodkin Jan
References (14)
14 references, click to expand
  1. Rapid assessment of extremal statistics for gapped local alignment.
    Proc Int Conf Intell Syst Mol Biol. 1999;:211-22 PMID: 10786304
  2. The estimation of statistical parameters for local alignment score distributions.
    Nucleic Acids Res. 2001 Jan 15;29(2):351-61 PMID: 11139604
  3. Discovering common stem-loop motifs in unaligned RNA sequences.
    Nucleic Acids Res. 2001 May 15;29(10):2135-44 PMID: 11353083
  4. Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.
    J Mol Biol. 2002 Mar 22;317(2):191-203 PMID: 11902836
  5. Alignment of RNA base pairing probability matrices.
    Bioinformatics. 2004 Sep 22;20(14):2222-7 PMID: 15073017
  6. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  7. GenBank.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D34-8 PMID: 15608212
  8. Compilation of tRNA sequences and sequences of tRNA genes.
    Nucleic Acids Res. 1998 Jan 1;26(1):148-53 PMID: 9399820
  9. MatrixPlot: visualizing sequence constraints.
    Bioinformatics. 1999 Sep;15(9):769-70 PMID: 10498780
  10. A probabilistic model for the evolution of RNA structure.
    BMC Bioinformatics. 2004 Oct 26;5:166 PMID: 15507142
  11. Fast and reliable prediction of noncoding RNAs.
    Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9 PMID: 15665081
  12. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.
    Bioinformatics. 2005 May 1;21(9):1815-24 PMID: 15657094
  13. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.
    Science. 2005 May 20;308(5725):1149-54 PMID: 15790807
  14. Finding the most significant common sequence and structure motifs in a set of RNA sequences.
    Nucleic Acids Res. 1997 Sep 15;25(18):3724-32 PMID: 9278497
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gki473
Published
2005-07-01
Pages
W650-3
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1160234
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gki473 PMC Full Text View journal details
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