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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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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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Implication

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

Cite This Study

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

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Discussion

Implication

Cite This Study

MAFFT version 5: improvement in accuracy of multiple sequence alignment

Key Points

Discussion

Implication

Cite This Study

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