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Related Experiment Videos

STRAP: editor for STRuctural Alignments of Proteins.

C Gille1, C Frömmel

  • 1Institute of Biochemistry, Charité, Medical Faculty of the Humboldt University, Monbijoustrasse 2a, 10117 Berlin, Germany.

Bioinformatics (Oxford, England)
|April 13, 2001
PubMed
Summary
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STRAP is a user-friendly tool for protein sequence alignment, incorporating structural data for improved accuracy. It efficiently manages large datasets and integrates with popular protein viewers.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Multiple sequence alignment is crucial for understanding protein function and evolution.
  • Integrating structural information can enhance alignment accuracy, especially for distantly related proteins.
  • Existing tools may lack user-friendliness or efficient handling of large datasets.

Purpose of the Study:

  • To introduce STRAP, a novel tool for generating and refining protein sequence alignments.
  • To highlight STRAP's unique feature of visualizing spatial distances for incorporating structural information.
  • To demonstrate STRAP's capability in managing large-scale alignments and its extensibility.

Main Methods:

  • STRAP supports multiple input file formats (SwissProt, GenBank, EMBL, DSSP, PDB, MSF, ASCII).

Related Experiment Videos

  • It features a unique visualization of C(alpha)-atom spatial distances within the alignment.
  • STRAP embeds protein viewers (INSIGHT, RASMOL, WEBMOL) and is written in JAVA.

    • Main Results:

    • STRAP provides a comfortable and extensible platform for protein sequence alignment.
    • The spatial distance visualization aids in incorporating structural information, guiding alignment for low similarity sequences.
    • The tool efficiently manages large alignments and integrates with external visualization software.

    Conclusions:

    • STRAP offers a valuable, user-friendly approach to protein sequence alignment by integrating structural data.
    • Its design facilitates easy adaptation and potential development into more complex alignment tools.
    • STRAP enhances the process of multiple sequence alignment, particularly for challenging datasets.