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Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences.
An infinite sequence of real numbers (in blue). This sequence is neither increasing, decreasing, convergent, nor Cauchy. It is, however, bounded. In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called elements, or terms).
The multiple sequence alignment problem is generally based on pairwise sequence alignment and currently, for a pairwise sequence alignment problem, biologists can use a dynamic programming approach to obtain its optimal solution. However, the multiple sequence alignment problem is still one of the more challenging problems in bioinformatics.
Clustal aligns sequences using a heuristic that progressively builds a multiple sequence alignment from a set of pairwise alignments. This method works by analyzing the sequences as a whole and using the UPGMA/neighbor-joining method to generate a distance matrix. A guide tree is calculated from the scores of the sequences in the matrix, then ...
Example multiple sequence alignment. There are millions of protein and nucleotide sequences known. These sequences fall into many groups of related sequences known as protein families or gene families. Relationships between these sequences are usually discovered by aligning them together and assigning this alignment a score.
M-Coffee: a special mode of T-Coffee that makes it possible to combine the output of the most common multiple sequence alignment packages (Muscle, ClustalW, Mafft, ProbCons, etc.). The resulting alignments are slightly better than the individual one, but most importantly the program indicates the alignment regions where the various packages ...
In bioinformatics, MAFFT (multiple alignment using fast Fourier transform) is a program used to create multiple sequence alignments of amino acid or nucleotide sequences. Published in 2002, the first version used an algorithm based on progressive alignment , in which the sequences were clustered with the help of the fast Fourier transform . [ 2 ]
In the shortest common supersequence problem, two sequences X and Y are given, and the task is to find a shortest possible common supersequence of these sequences. In general, an SCS is not unique. For two input sequences, an SCS can be formed from a longest common subsequence (LCS) easily.