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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 CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
- J. Thompson, T. Gibson, F. Plewniak, F. Jeanmougin, D. Higgins
- Biology, MedicineNucleic acids research
- 1 December 1997
ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Clustal W and Clustal X version 2.0
- Mark A. Larkin, G. Blackshields, +10 authors D. Higgins
- Computer Science, MedicineBioinform.
- 1 November 2007
SUMMARY The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future…
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
- Fabian Sievers, A. Wilm, +9 authors D. Higgins
- Biology, MedicineMolecular systems biology
- 11 October 2011
A new program called Clustal Omega is described, which can align virtually any number of protein sequences quickly and that delivers accurate alignments, and which outperforms other packages in terms of execution time and quality.
Multiple sequence alignment with the Clustal series of programs
The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the…
Multiple sequence alignment with Clustal X.
Multiple Sequence Alignment Using ClustalW and ClustalX
- J. Thompson, T. Gibson, D. Higgins
- Computer Science, MedicineCurrent protocols in bioinformatics
- 1 January 2003
The protocols in this unit discuss how to use ClustalX and ClUSTalW to construct an alignment, and create profile alignments by merging existing alignments.
Using CLUSTAL for multiple sequence alignments.
It is argued that using one weight matrix and two gap penalties is too simplistic to be of general use in the most difficult cases and a large number of new parameters designed primarily to help encourage gaps in loop regions are replaced.
Protein disorder prediction: implications for structural proteomics.
- R. Linding, L. Jensen, F. Diella, P. Bork, T. Gibson, R. Russell
- Biology, MedicineStructure
- 1 November 2003
DisEMBL is a computational tool for prediction of disordered/unstructured regions within a protein sequence that has developed parameters based on several alternative definitions and introduced a new one based on the concept of "hot loops," i.e., coils with high temperature factors.
Ancient Protostome Origin of Chemosensory Ionotropic Glutamate Receptors and the Evolution of Insect Taste and Olfaction
It is shown that IRs are expressed in olfactory organs across Protostomia—a major branch of the animal kingdom that encompasses arthropods, nematodes, and molluscs—indicating that they represent an ancestral protostome chemosensory receptor family.