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Enhance the accuracy and scalability of the MAFFT multiple sequence alignment program by implementing novel iterative refinement algorithms and homologous sequence integration.

January 19, 2005Nucleic Acids ResearchOpen Access

MAFFT version 5: improvement in accuracy of multiple sequence alignment

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KKKazutaka KatohThe University of Tokyo

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Implication

Algorithm evaluation reveals improved accuracy and scalability in large sequence datasets, suggesting enhanced utility for evolutionary and structural biology.

Key Points

Enhance the accuracy and scalability of the MAFFT multiple sequence alignment program by implementing novel iterative refinement algorithms and homologous sequence integration.
Introduced new iterative refinement options (H-INS-i, F-INS-i, and G-INS-i) that incorporate pairwise alignment information into the objective function.
Benchmarked MAFFT version 5.3 against T-Coffee version 2 and CLUSTAL W using datasets containing more than 50 sequences on standard desktop computers.
Evaluated accuracy gains by integrating close homologues (E-value < 10^-5 to 10^-20) retrieved from SwissProt via NCBI-BLAST using the mafftE.rb script.
The new iterative refinement options in MAFFT achieved higher alignment accuracy than T-Coffee v2 and CLUSTAL W in benchmark tests of more than 50 sequences.
Including dozens of close database homologues improved multiple alignment accuracy by 2 to 10 percentage points for sets of approximately 8 low-similarity sequences.

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Kazutaka Katoh (2005) studied this question.

synapsesocial.com/papers/69d6cab58dca315383ed8f75 https://doi.org/10.1093/nar/gki198

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Implication

Algorithm evaluation reveals improved accuracy and scalability in large sequence datasets, suggesting enhanced utility for evolutionary and structural biology.

MAFFT version 5: improvement in accuracy of multiple sequence alignment

Discussion

Member takes

Implication

Key Points

Cite This Study

MAFFT version 5: improvement in accuracy of multiple sequence alignment

Discussion

Member takes

Implication

Key Points

Cite This Study

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