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SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.

Hongyi Zhou1, Yaoqi Zhou

  • 1Department of Physiology and Biophysics, Howard Hughes Medical Institute Center for Single Molecule Biophysics, State University of New York, Buffalo, NY 14214, USA.

Bioinformatics (Oxford, England)
|July 16, 2005
PubMed
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SPEM improves multiple sequence alignment accuracy for remote homologs by 7-15% using sequence profiles and predicted secondary structures. This bioinformatics tool offers enhanced alignment for evolutionary studies.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate multiple sequence alignment is crucial for genome-scale studies of gene evolution.
  • Aligning remote homologous sequences presents a significant bioinformatics challenge.
  • Existing methods struggle with accuracy when dealing with distantly related sequences.

Purpose of the Study:

  • To develop a novel method, SPEM, for enhanced multiple sequence alignment.
  • To improve the accuracy of aligning remote homologous sequences.

Main Methods:

  • SPEM utilizes pre-processed sequence profiles and predicted secondary structures for initial pairwise alignments.
  • A consistency-based scoring system refines these pairwise alignments.
  • A progressive algorithm is employed for the final multiple sequence alignment.

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Main Results:

  • SPEM demonstrated a 7-15% higher average sum of pairwise alignment scores compared to established methods (ClustalW, T-Coffee, MUSCLE, ProbCons, PRALINE(PSI)) for remote homologs (sequence identity <30%).
  • For homologous sequences (sequence identity >30%), SPEM's accuracy was statistically comparable to state-of-the-art methods like ProbCons and MUSCLE 6.0.
  • SPEM shows significant improvement in aligning evolutionarily distant sequences.

Conclusions:

  • SPEM offers a substantial advancement in multiple sequence alignment accuracy, particularly for challenging remote homologs.
  • The method provides a valuable tool for genomic and evolutionary bioinformatics research.
  • SPEM is available as a server and executables for broader scientific use.