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ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments.

Matthias Wolf1, Benjamin Ruderisch, Thomas Dandekar

  • 1Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany. matthias.wolf@biozentrum.uni-wuerzburg.de

Bioinformatics (Oxford, England)
|August 30, 2008
PubMed
Summary
This summary is machine-generated.

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The Profile Neighbor Joining (PNJ) algorithm in ProfDistS reconstructs large phylogenetic trees efficiently using RNA secondary structures. This method supports sequence-structure alignments for both RNA and protein sequences.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Phylogenetics

Background:

  • The Profile Neighbor Joining (PNJ) algorithm offers computational efficiency for reconstructing large phylogenetic trees.
  • RNA secondary structures are crucial for RNA alignment analysis and phylogenetic reconstruction.
  • Existing methods may not fully integrate sequence and structure data effectively.

Purpose of the Study:

  • To present ProfDistS, a phylogenetic workflow integrating RNA secondary structures into phylogenetic reconstruction.
  • To leverage the PNJ algorithm for sequence-structure alignments.
  • To provide a robust tool for analyzing both RNA and protein sequence data.

Main Methods:

  • Utilizing the Profile Neighbor Joining (PNJ) algorithm within the ProfDistS software.

Related Experiment Videos

  • Employing sequence-structure alignments for phylogenetic analysis.
  • Implementing manual, iterative, and automatic profile definition methods.
  • Extending the workflow to accommodate protein sequences.

    • Main Results:

    • ProfDistS successfully reconstructs phylogenies using individual RNA secondary structures.
    • The workflow effectively handles sequence-structure alignments via PNJ.
    • ProfDistS demonstrates versatility by processing both RNA and protein sequences.
    • The software provides a comprehensive phylogenetic workflow.

    Conclusions:

    • ProfDistS offers an efficient and integrated approach to phylogenetic reconstruction using sequence-structure data.
    • The tool enhances the analysis of RNA and protein evolution.
    • ProfDistS represents a significant advancement in bioinformatics tools for phylogenetic analysis.