First 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms. Generated with ClustalX.
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. Alignments highlight mutation events such as point mutations (single amino acid or nucleotide changes), insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides.
Multiple sequence alignments require more sophisticated methodologies than pairwise alignments, as they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. However, heuristic methods generally cannot guarantee high-quality solutions and have been shown to fail to yield near-optimal solutions on benchmark test cases.[1][2][3]
^Thompson JD, Linard B, Lecompte O, Poch O (2011). "A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives". PLOS ONE. 6 (3): e18093. Bibcode:2011PLoSO...618093T. doi:10.1371/journal.pone.0018093. PMC 3069049. PMID 21483869.
^Cite error: The named reference nuin2006 was invoked but never defined (see the help page).
^Hosseininasab A, van Hoeve WJ (2019). "Exact Multiple Sequence Alignment by Synchronized Decision Diagrams". INFORMS Journal on Computing. doi:10.1287/ijoc.2019.0937. S2CID 109937203.
and 24 Related for: Multiple sequence alignment information
In bioinformatics, a sequencealignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence...
of sequencealignment software is a compilation of software tools and web portals used in pairwise sequencealignment and multiplesequencealignment. See...
acid or protein sequence as input, or use statistical models generated from multiplesequencealignments of known related sequences. Statistical models...
Clustal is a computer program used for multiplesequencealignment in bioinformatics. The software (and algorithms) have gone through several iterations...
Sequence logos provide a compact and informative visualization of conserved sequence and variability. Multiplesequencealignment: Multiplesequence alignment...
(for multiplealignment using fast Fourier transform) is a program used to create multiplesequencealignments of amino acid or nucleotide sequences. Published...
homologous to the sequences that were used to construct the profile-HMM. Profile-HMMs are constructed from a multiplesequencealignment in the HMMER package...
This page is a subsection of the list of sequencealignment software. Multiplealignment visualization tools typically serve four purposes: Aid general...
then obtain the local alignment. Multiplesequencealignment is an extension of pairwise alignment to align several sequences at a time. Different MSA...
at each position in a sequencealignment. It represents the results of multiplesequencealignments in which related sequences are compared to each other...
which multiple unrelated amino acid sequences converge on a common tertiary structure. Structural alignments can compare two sequences or multiple sequences...
techniques that provide the sequence comparisons (sequencealignment) and analyze the alignment product to understand its biology. Sequence analysis in molecular...
method of scoring alignments of two or more sequences. When aligning sequences, introducing gaps in the sequences can allow an alignment algorithm to match...
generate multiplesequencealignments.[page needed] This method utilizes Kmer and Kimura distances to generate multiplesequencealignments.[page needed]...
2014). "AliGROOVE--visualization of heterogeneous sequence divergence within multiplesequencealignments and detection of inflated branch support". BMC...
nucleic acid secondary structures can be used to aid in multiplesequencealignment. These alignments can be made more accurate by the inclusion of secondary...
Sequence graph, also called an alignment graph, breakpoint graph, or adjacency graph, are bidirected graphs used in comparative genomics. The structure...
Bauer M, Klau GW, Reinert K (July 2007). "Accurate multiplesequence-structure alignment of RNA sequences using combinatorial optimization". BMC Bioinformatics...
used to calculate the likelihood of phylogenetic trees using multiplesequencealignment data. Thus, substitution models are central to maximum likelihood...
situation improves somewhat when the amino acid variation in multiplesequencealignments is taken into account. Some parts of the protein have fixed three-dimensional...
may be protein sequences or nucleic acid sequences, and they can contain gaps or alignment characters (see sequencealignment). Sequences are expected to...
Global Information