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Related Experiment Videos

Playing with blocks: some pitfalls of forcing multiple alignments.

S Henikoff1

  • 1Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98104.

The New Biologist
|December 1, 1991
PubMed
Summary
This summary is machine-generated.

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Block alignments of amino acid sequences help identify protein function. However, ad hoc methods can be misleading, so results require careful validation, especially when standard methods fail without human intervention.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Multiple amino acid sequence alignments represent regions of shared ancestry and function.
  • Protein sequence similarity often suggests functional similarity within protein families.

Purpose of the Study:

  • To analyze the potential pitfalls and biases in block alignment methods.
  • To evaluate the validity of proposed protein relationships based on sequence alignments.

Main Methods:

  • Analysis of examples from scientific literature illustrating problems in block alignment.
  • Critical examination of visual and computer-aided alignment techniques.
  • Assessment of alignment validity in the context of controls.

Main Results:

Related Experiment Videos

  • Ad hoc methods for generating block alignments can lead to difficulties in validating proposed protein relationships.
  • Visual inspection of alignments can be deceptive without proper controls.
  • Computer-aided methods may introduce biases, yielding misleading results.

Conclusions:

  • Block alignments generated by standard methods that require significant human intervention should be treated with caution.
  • Careful validation is essential when interpreting the functional or evolutionary significance of block alignments.
  • The reliability of sequence alignment tools depends on their ability to avoid introducing biases.