(2006). Multiple Sequence Alignment. In: Introduction to Computational Biology. Birkhäuser Basel. https://doi.org/10.1007/3-7643-7387-3_5 Download citation .RIS DOIhttps://doi.org/10.1007/3-7643-7387-3_5 Publisher NameBirkhäuser Basel Online ISBN...
The alignment of protein sequences is the most powerful computational tool available to the molecular biologist. Where one sequence is of unknown structure and function, its alignment with another sequence that is well characterized in both structure and
Multiple sequence alignment (MSA) is an important step in comparative sequence analyses. Parallelization is a key technique for reducing the time required for large-scale sequence analyses. The three calculation stages, all-to-all comparison, progressive alignment and iterative refinement, of the MAFFT...
This paper presents an approach to the multiple sequence alignment (MSA) problem by applying genetic algorithms with a reserve selection mechanism. MSA is one of the most fundamental operations in bioinformatics, which plays an important part in predicting the structure, function and evolution of biol...
We denote byxi ∈ {1, …, q} the state of sitei ∈ {1, …, L}, whereq = 21 is the number of possible states, namely the 20 natural amino acids and the alignment gap. A general Potts model Hamiltonian applied to a sequencex = (x1, …, xL) ...
Sequence similarity search, multiple sequence alignment, model selection, distance matrix and phylogeny reconstruction. Nature Protocol Exchange, Published online 11 July 2013. http://dx.doi. org/10.1038/protex.2013.065.Bast F (2013) Sequence similarity search, multiple sequence alignment, model ...
This paper deals with Multiple Sequence Alignment (MSA) and the difficulties to derive optimal results from computer algorithms, especially when comparing hundreds of sequences or more. It is common to improve outputs of computer MSA with manual alignment, because humans can find badly aligned areas...
MSAVis depicts aligned protein sequences, the strength of the alignment, and the conserved domains over the collected proteins. Starting from a pre-calculated alignment provided by the user in ClustalW [1] or PHYLIP [15] format, MSAVis queries the online NCBI CDD for each sequence and parse...
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The problem of simultaneously aligning a number of sequences is referred to as multiple sequence alignment. We provide a dynamic programming algorithm for multiple alignment which extends the dynamic programming algorithm for global pairwise alignment. W