Search results
Results from the WOW.Com Content Network
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.
Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple alignment methods try to align all of the sequences in a given query set. Multiple alignments are often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related.
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.
A sequence logo for the LexA-binding motif of gram-positive bacteria. As the adenosine at position 5 is highly conserved, it appears larger than other characters. [29] Multiple sequence alignments can be used to visualise conserved sequences.
A guide tree is calculated from the scores of the sequences in the matrix, then subsequently used to build the multiple sequence alignment by progressively aligning the sequences in order of similarity. [15] Clustal creates multiple sequence alignments through three main steps: Complete a pairwise alignment using the progressive alignment method.
The gap information is usually used in the form of indel frequency profiles, which is more specific for the sequences to be aligned. ClustalW and MAFFT adopted this kind of gap penalty determination for their multiple sequence alignments. [13] Alignment accuracies can be improved using this model, especially for proteins with low sequence identity.
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 ]
A profile HMM modelling a multiple sequence alignment. HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. [2] Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments.