Multiple sequence alignments are often computed for known members of a protein family. The aim is to discover sequence motifs that are conserved across the mem bers of the protein family in order to infer the functionally important protein domains. Like
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. We describe frequency based algorithms to align a se...
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...
We introduce the online server for PRALINE (http://ibium.cs.vu.nl/programs/pralinewww/), an iterative versatile progressive multiple sequence alignment (MSA) tool. PRALINE provides various MSA optimisation strategies including weighted global and local profile pre-processing, secondary structure-guided...
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) ...
Multiple sequence alignment using the Hidden Markov Model trained by an improved quantum-behaved particle swarm optimization[J] . Jun Sun,Xiaojun Wu,Wei Fang,Yangrui Ding,Haixia Long,Webo Xu.Information Sciences . 2010 (1)Multiple sequence alignment using the Hidden Markov Model trained by an ...
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...
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Alignment (pairwise and multiple) is central in the comparison of biological sequences. Some of the purposes in aligning sequences are:...