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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
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Adding unaligned sequences into an existing alignment using MAFFT and LAST.

Kazutaka Katoh1, Martin C Frith

  • 1Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita 565-0871, Japan. katoh@ifrec.osaka-u.ac.jp

Bioinformatics (Oxford, England)
|October 2, 2012
PubMed
Summary
This summary is machine-generated.

The MAFFT package now offers two methods for adding unaligned sequences to multiple sequence alignments. The '--addfragments' option accurately aligns even short, fragmentary sequences, outperforming other methods in challenging scenarios.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment is crucial for evolutionary and functional inference.
  • Existing methods struggle with incorporating unaligned or fragmentary sequences.

Purpose of the Study:

  • To introduce and evaluate new methods for adding unaligned sequences into existing multiple sequence alignments within the MAFFT package.
  • To compare the performance of these new methods against existing tools like PaPaRa and PAGAN.

Main Methods:

  • Implementation of two new options, '--add' and '--addfragments', in the MAFFT package.
  • Methods infer phylogenetic relationships to position unaligned sequences accurately.
  • Benchmarking using two independent simulations to assess accuracy.

Main Results:

  • The '--addfragments' option demonstrates superior accuracy for difficult alignment problems involving fragmentary sequences.
  • Both '--add' and '--addfragments' methods show appropriate handling of easier alignment tasks.
  • Performance comparison indicates '--addfragments' outperforms PaPaRa and PAGAN in accuracy for challenging datasets.

Conclusions:

  • The '--addfragments' option provides a significant advancement for incorporating diverse sequence data into multiple sequence alignments.
  • MAFFT's new methods offer robust solutions for handling both full-length and fragmentary unaligned sequences.
  • These tools enhance the utility of MAFFT for phylogenetic and comparative genomic analyses.