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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
- Computer Science, BiologyNucleic 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.
Multiple sequence alignment with Clustal X.
Using CLUSTAL for multiple sequence alignments.
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches.
The rapidity and reliability of DbClustal have been demonstrated using the recently annotated Pyrococcus abyssi proteome where the number of alignments with totally misaligned sequences was reduced from 20% to <2%.
Towards a reliable objective function for multiple sequence alignments.
- J. Thompson, F. Plewniak, R. Ripp, J. Thierry, O. Poch
- BiologyJournal of molecular biology
- 7 December 2001
NeitherMD combines the advantages of the column-scoring techniques with the sensitivity of methods incorporating residue similarity scores, and incorporates ab initio sequence information, such as the number, length and similarity of the sequences to be aligned.
The KH domain occurs in a diverse set of RNA‐binding proteins that include the antiterminator NusA and is probably involved in binding to nucleic acid
PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames.
A dynamic alignment algorithm is reported here which compares a protein profile (a residue scoring matrix for one or more aligned sequences) against the three translation frames of a DNA strand, allowing frameshifting.
The PH domain: a common piece in the structural patchwork of signalling proteins.
BRCA1 mutations in a population-based sample of young women with breast cancer.
- A. Langston, K. Malone, J. Thompson, J. Daling, E. Ostrander
- Medicine, BiologyThe New England journal of medicine
- 18 January 1996
These results represent a minimal estimate of the frequency of BRCA1 mutations in this population of young women with breast cancer and show the risk of harboring a mutation was not limited to women with family histories of breast or ovarian cancer.