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Related Experiment Videos

JAE: Jemboss Alignment Editor.

Tim J Carver1, Lisa J Mullan

  • 1The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. tjc@sanger.ac.uk

Applied Bioinformatics
|September 1, 2005
PubMed
Summary
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The Jemboss Alignment Editor (JAE) enhances sequence alignment analysis by enabling manual editing and visualization of sequence similarity. This free tool aids researchers in understanding biological significance through intuitive sequence alignment interpretation.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Understanding biological significance often relies on sequence alignment.
  • Manual editing of alignments generated by software is crucial for accuracy.
  • The European Molecular Biology Open Source Software Suite (EMBOSS) provides bioinformatics tools.

Purpose of the Study:

  • To introduce the Jemboss Alignment Editor (JAE) as a new tool for manual sequence alignment editing.
  • To provide a freely available resource for enhancing sequence alignment analysis within the Jemboss package.

Main Methods:

  • The Jemboss Alignment Editor (JAE) offers standard editing functionalities.
  • It incorporates residue and nucleotide coloring to highlight regions of interest.

Related Experiment Videos

  • Utilizes scoring matrices (PAM and BLOSUM) for visualizing similarity and identity.

    • Main Results:

    • JAE facilitates the display of regions with high similarity and identity using selected scoring matrices.
    • The tool includes features for calculating consensus sequences and consensus plots.
    • Pairwise identity calculations are also supported.

    Conclusions:

    • The Jemboss Alignment Editor (JAE) is a valuable, freely accessible tool for researchers in bioinformatics.
    • It improves the process of interpreting biological significance through enhanced sequence alignment visualization and editing.
    • JAE integrates seamlessly into the EMBOSS software suite.