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

Jakob H Havgaard1, Rune B Lyngsø, Jan Gorodkin

  • 1Center for Bioinformatics and Division of Genetics, IBHV, The Royal Veterinary and Agricultural University Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

Nucleic Acids Research
|June 28, 2005
PubMed
Summary

This study presents a web server for RNA sequence structural alignment using the updated Foldalign algorithm. It enables efficient identification of common structural motifs or global/local alignment of entire RNA sequences.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • RNA structural alignment is crucial for understanding RNA function and evolution.
  • Existing algorithms may lack user-friendly interfaces for complex structural alignments.

Purpose of the Study:

  • To introduce a web server implementing the updated Foldalign algorithm for pairwise RNA structural alignment.
  • To provide a user-friendly platform for identifying RNA structural motifs and aligning RNA sequences.

Main Methods:

  • Utilized the Sankoff-based Foldalign algorithm for structural RNA sequence alignment.
  • Developed a web server with a graphical interface for pairwise sequence analysis.
  • Enabled local, global, and motif-based alignment options.

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Main Results:

  • The web server facilitates the alignment of two RNA sequences based on structural information.
  • Users can efficiently scan for common structural motifs or perform comprehensive sequence alignments.
  • The graphical interface simplifies the alignment process and result visualization.

Conclusions:

  • The Foldalign web server offers a valuable tool for RNA structural bioinformatics research.
  • Its intuitive interface and flexible alignment options enhance the study of RNA structure-function relationships.