Contextual multiple sequence alignment.
Anna Gambin,Rafał Otto +1 more
TL;DR: A contextual multiple alignment algorithm is presented and the outcomes of experiments performed for the BAliBASE test set are reported and the contextual approach turned out to give much better results for the set of sequences containing orphan genes.
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Abstract: In a recently proposed contextual alignment model, efficient algorithms exist for global and local pairwise alignment of protein sequences. Preliminary results obtained for biological data are very promising. Our main motivation was to adopt the idea of context dependency to the multiple alignment setting. To this aim the relaxation of the model was developed (we call this new model averaged contextual alignment) and a new family of amino acids substitution matrices are constructed. In this paper we present a contextual multiple alignment algorithm and report the outcomes of experiments performed for the BAliBASE test set. The contextual approach turned out to give much better results for the set of sequences containing orphan genes.
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Citations
Sequence context-specific profiles for homology searching.
Andreas Biegert,Johannes Söding +1 more
TL;DR: This work presents an approach that derives context-specific amino acid similarities from short windows centered on each query sequence residue that can replace substitution matrices in sequence- and profile-based alignment and search methods for both protein and nucleotide sequences.
198
Hierarchical clustering based upon contextual alignment of proteins: a different way to approach phylogeny
Anna Gambin,Piotr P. Slonimski +1 more
TL;DR: The contextual alignment scores calculated in this model were used to hierarchical clustering of several protein families from the database of Clusters of Orthologous Groups (COG), and shows that the contextual model results in more consistent clustering trees.
12
•Dissertation
Context-specific methods for sequence homology searching and alignment
Andreas Biegert
- 13 Dec 2010
2
Design of potential cellulase primer using multiple sequence alignment method
Bahrul Ulum,Wisnu Ananta Kusuma,Joni Prasetyo +2 more
- 05 Jan 2013
TL;DR: This research performs alignment of DNA sequences coding of cellulase to look for potential primer in order to increase the productivity of cellulases enzymes by Multiple Sequence Alignment (MSA) method.
References
Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: 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 neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Amino acid substitution matrices from protein blocks
TL;DR: This work has derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins, leading to marked improvements in alignments and in searches using queries from each of the groups.
7.2K
•Book
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
Richard Durbin,Sean R. Eddy,Anders Krogh,Graeme Mitchison +3 more
- 01 Feb 2005
TL;DR: This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis.
4.5K
A comprehensive comparison of multiple sequence alignment programs
TL;DR: This paper presents the first systematic study of the most commonly used alignment programs using BAliBASE benchmark alignments as test cases, and proposes appropriate alignment strategies, depending on the nature of a particular set of sequences.