Abstract：
: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. The method is broadly based on the popular progressive approach to multiple alignment but avoids the most serious pitfalls caused by the greedy nature of this algorithm. With T-Coffee we pre-process a data set of all pair-wise alignments between the sequences. This provides us with a library of alignment information that can be used to guide the progressive alignment. Intermediate alignments are then based not only on the sequences to be aligned next but also on how all of the sequences align with each other. This alignment information can be derived from heterogeneous sources such as a mixture of alignment programs and/or structure superposition. Here, we illustrate the power of the approach by using a combination of local and global pair-wise alignments to generate the library. 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 the sequences in the tests.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Notredame C,Higgins DG,Heringa Jdoi
10.1006/jmbi.2000.4042keywords:
subject
Has Abstractpub_date
2000-09-08 00:00:00pages
205-17issue
1eissn
0022-2836issn
1089-8638pii
S0022-2836(00)94042-7journal_volume
302pub_type
杂志文章abstract：:Biochemical functions of proteins in cells frequently involve interactions with various ligands. Proteomic methods for the identification of proteins that interact with specific ligands such as metabolites, signaling molecules, and drugs are valuable in investigating the regulatory mechanisms of cellular metabolism, a...
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pub_type： 杂志文章,评审
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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