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Related Experiment Videos

PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments.

Daniel R Caffrey1, Paul H Dana, Vidhya Mathur

  • 1Pfizer Global Research and Development, 620 Memorial Drive, Cambridge, MA 02139, USA. daniel.caffrey@gmail.com

BMC Bioinformatics
|October 13, 2007
PubMed
Summary
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The Protein Family Alignment and Analysis Tool (PFAAT) version 2.0 facilitates the analysis of protein sequence alignments through enhanced annotation features. This tool aids in understanding protein family relationships and functions.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Homologous sequences share structural and functional similarities due to common ancestry.
  • Multiple sequence alignments are crucial for identifying functional trends.
  • Integrating structural and phylogenetic analysis enhances alignment studies.

Purpose of the Study:

  • Introduce PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments.
  • Highlight the new framework supporting multiple annotations for enhanced functionality.
  • Enable sophisticated analysis by linking sequence annotations with residue properties.

Main Methods:

  • Utilizing multiple sequence alignments with manual or automated sequence annotations (e.g., from UniProt).

Related Experiment Videos

  • Implementing a sophisticated search dialog for selecting and sorting sequences based on annotations.
  • Applying statistical methods to model relationships between annotations and residue properties.
  • Incorporating novel algorithms for sequence conservation computation and visualization.

    • Main Results:

    • PFAAT 2.0 supports multiple sequence annotations, accessible from alignment and tree views.
    • Annotations can be manually created or automatically extracted, facilitating sequence selection and sorting.
    • Residue annotations enable targeted analysis of specific alignment columns, such as percent identity calculation.
    • New features include conservation analysis, 3D structure mapping, secondary structure display, and composition-based sorting.

    Conclusions:

    • PFAAT provides a framework for users to annotate protein family knowledge.
    • Annotations integrated with advanced analyses facilitate hypothesis testing related to sequence, structure, and function.