COFFEE: an objective function for multiple sequence alignments

By Cédric Notredame, Liisa Holm, Desmond G. Higgins. 1998

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, background): “D i st a n c e i s e st i m a t e d b a s e d o n D P .”
ProbCons: Probabilistic consistency-based multiple sequence alignment. (2005, background): “More recently, Notredame et al. (1998) introduced COFFEE, a new consistency-based objective function for scoring residue pairs in a pairwise alignment.”
Recent developments in the MAFFT multiple sequence alignment program (2008, methodology): “Due to the increasing necessity for MSA of distant homologs, in 2005, we sought to improve the accuracy of MAFFT, and released Version 5 [14], which adopted a new objective function, the summation of a traditional weighted sum-of-pairs (WSP) score [24], and a consistency score similar to COFFEE [25]”
Multiple sequence alignment using partial order graphs (2002, background): “…sequences be aligned in 'the right order' (i.e. most similar sequences first), because there is no algorithmic guarantee that the overall alignment process will actually find an optimal alignment for any given sequence (Higgins and Sharp, 1988; Mevissen and Vingron, 1996; Notredame et al., 1998).”
A simple method to control over-alignment in the MAFFT multiple sequence alignment program (2016, background): “In each step of the group-to-group alignment calculation, we can estimate the expected evolutionary distance d IJ between the groups I and J as 2 (cid:2) the branch length from the node to its descendant termini.”
The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana (2004, methodology): “Predicted proteins for all gene families were aligned using T-Coffee [ 19 ] and a maximum of 30 randomly selected proteins sequences from each family.”
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (2008, background): “With the second term, Consistency, a multiple alignment is evaluated with respect to its consistency with the pairwise alignments [39].”
M-Coffee: combining multiple sequence alignment methods with T-Coffee (2006, methodology): “03 uses a consistency-based objective function (27) optimized using progressive alignment.”
AL2CO: calculation of positional conservation in a protein sequence alignment (2001, background): “Analysis of positional conservation in an amino acid sequence alignment can aid in detection of motifs and functionally and/or structurally important residues, e.g. at the binding sites (Zuckerkandl and Pauling, 1965; Villar and Kauvar, 1994; Ouzounis et al., 1998).”
T-Coffee: A novel method for fast and accurate multiple sequence alignment. (2000, background): “We use the structure described by Notredame et al. (1998).”