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Related Experiment Videos

A reality check for alignments and trees.

William Martin1, Mayo Roettger, Peter J Lockhart

  • 1Institute of Botany III, University of Düsseldorf, Düsseldorf, Germany. w.martin@uni-duesseldorf.de

Trends in Genetics : TIG
|September 11, 2007
PubMed
Summary
This summary is machine-generated.

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Sequence alignment direction impacts biological results. Processing sequences from C-terminus to N-terminus can yield different multiple sequence alignments and phylogenetic trees compared to the standard N-terminus to C-terminus method.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Evolution

Background:

  • Multiple sequence alignment is a fundamental technique in bioinformatics.
  • Standard alignment methods process sequences from N-terminus to C-terminus.
  • The directionality of sequence processing can influence alignment outcomes.

Purpose of the Study:

  • To investigate the impact of sequence processing direction on multiple sequence alignment.
  • To determine if altering alignment direction affects downstream phylogenetic analyses.
  • To introduce methods for assessing the reliability of sequence alignments.

Main Methods:

  • Generating multiple sequence alignments using both N-to-C and C-to-N terminal processing.
  • Comparing alignment results obtained from different processing directions.

Related Experiment Videos

  • Constructing phylogenetic trees from the generated alignments.

    • Main Results:

    • Different multiple sequence alignments were obtained when processing sequences in reverse (C-to-N) compared to the standard (N-to-C) direction.
    • The choice of alignment direction can lead to variations in resulting phylogenetic trees.
    • The study provides practical approaches to evaluate the consistency and reliability of sequence alignments.

    Conclusions:

    • Sequence alignment direction is a critical factor in molecular evolutionary studies.
    • The findings underscore the importance of considering alignment methodology for accurate phylogenetic inference.
    • New methods are proposed to enhance the trustworthiness of sequence alignment in biological research.