T-Coffee: A novel method for fast and accurate multiple sequence alignment.

@article{Notredame2000TCoffeeAN,
  title={T-Coffee: A novel method for fast and accurate multiple sequence alignment.},
  author={C. Notredame and Desmond G. Higgins and Jaap Heringa},
  journal={Journal of molecular biology},
  year={2000},
  volume={302 1},
  pages={
          205-17
        }
}
We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. [] Key Result The resulting alignments are significantly more reliable, as determined by comparison with a set of 141 test cases, than any of the popular alternatives that we tried. The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of…
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References

SHOWING 1-10 OF 37 REFERENCES

COFFEE: an objective function for multiple sequence alignments

It is shown that multiple sequence alignments can be optimized for their COFFEE score with the genetic algorithm package SAGA and given a library of structure-based pairwise alignments extracted from FSSP, SAG a can produce high-quality multiple sequencealignments.

Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments.

  • O. Gotoh
  • Biology
    Journal of molecular biology
  • 1996
The improvement in accuracy of alignments obtained by these iterative methods over pairwise or progressive method tends to increase with decreasing average sequence identity, implying that iterative refinement is more effective for the generally difficult alignment of remotely related sequences.

Multiple sequence alignment with the Divide-and-Conquer method.

Combining many multiple alignments in one improved alignment

A method that extracts qualitatively good sub-alignments from a set of multiple alignments and combines these into a new, often improved alignment, implemented as a variant of the traditional dynamic programming technique.

DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment

A modification of the weight function used in the original version of the alignment program DIALIGN has two important advantages: it can be applied to both globally and locally related sequence sets, and the running time of the program is considerably improved.

A tool for multiple sequence alignment.

The design and application of a tool for multiple alignment of amino acid sequences that implements a new algorithm that greatly reduces the computational demands of dynamic programming is described.

Two Strategies for Sequence Comparison: Profile-preprocessed and Secondary Structure-induced Multiple Alignment

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.

The multiple sequence alignment problem in biology

It is proved here that knowledge of the measure of an arbitrarily chosen alignment can be used in combination with information from the pairwise alignments to considerably restrict the size of the region of the lattice in consideration.

A branch-and-cut algorithm for multiple sequence alignment

This work considers a branch-and-cut approach for solving the multiple sequence alignment problem and shows that this method outperforms the best tools developed so far, in that it produces alignments that are better from a biological point of view.