Multiple sequence alignment
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more
- Comment
- enMultiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more
- Date
- 22 August 2010
- Depiction
- Has abstract
- enMultiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or nucleotides. Computational algorithms are used to produce and analyse the MSAs due to the difficulty and intractability of manually processing the sequences given their biologically-relevant length. MSAs require more sophisticated methodologies than pairwise alignment because 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. On the other hand, heuristic methods generally fail to give guarantees on the solution quality, with heuristic solutions shown to be often far below the optimal solution on benchmark instances.
- Hypernym
- Alignment
- Is primary topic of
- Multiple sequence alignment
- Label
- enMultiple sequence alignment
- Link from a Wikipage to an external page
- www.expasy.org/tools/%23align
- web.archive.org/web/20060909003117/http:/pbil.univ-lyon1.fr/alignment.html
- dialign.gobics.de/chaos-dialign-submission
- www.ch.embnet.org/software/ClustalW.html
- web.archive.org/web/20120305164700/http:/www.embl.de/~seqanal/courses/commonCourseContent/commonMsaExercises.html
- cmb.molgen.mpg.de/
- faculty.cs.tamu.edu/shsze/psalign/
- sourceforge.net/projects/msa-edna/
- sourceforge.net/projects/poamsa/files/
- www.clustal.org/
- www.ebi.ac.uk/Tools/clustalw2/
- www.ebi.ac.uk/Tools/kalign/
- www.ebi.ac.uk/Tools/mafft/
- www.ebi.ac.uk/Tools/muscle/
- www.ebi.ac.uk/Tools/t-coffee/
- www.genome.jp/tools/prrn/
- www.mergealign.com/
- www.tcoffee.org/
- www.tcoffee.org/Projects/mcoffee/
- web.archive.org/web/20060705082556/http:/align.genome.jp/
- web.archive.org/web/20130328131920/http:/blocks.fhcrc.org/
- www.ebi.ac.uk/Tools/clustalw2/index.html
- web.archive.org/web/20110904184621/http:/www.avatar.se/molbioinfo2001/index.html
- meme.sdsc.edu/meme/intro.html
- web.archive.org/web/20100822143504/http:/meme.sdsc.edu/meme/intro.html
- www.stevekellylab.com/software/mergealign
- web.archive.org/web/20090821192233/http:/bioinf.may.ie/school02/notes.html
- compbio.soe.ucsc.edu/sam.html
- tcoffee.crg.cat/tcs
- web.archive.org/web/20100107231637/http:/www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html
- Link from a Wikipage to another Wikipage
- Algorithm
- Alignment-free sequence analysis
- Amino acid
- Benders decomposition
- Big O notation
- Biological sequence
- Branch and price
- CASP
- Category:Bioinformatics
- Category:Computational phylogenetics
- Category:Markov models
- Cladistics
- Clustal
- Cluster analysis
- Computational complexity theory
- Conservation (genetics)
- Directed acyclic graph
- DNA
- D-Wave Systems
- Dynamic programming
- European Molecular Biology Laboratory
- Evolutionary
- Exons
- Expectation-maximization algorithm
- FASTA
- File:A profile HMM modelling a multiple sequence alignment.png
- File:Caspase-motif-alignment.png
- File:Non-homologous exon alignment.jpg
- File:RPLP0 90 ClustalW aln.gif
- Frameshift
- Gap penalty
- Generalized tree alignment
- Genetic algorithm
- Gibbs sampler
- Global optimization
- Graph (discrete mathematics)
- Heuristic
- HHsearch
- Hidden Markov model
- Hill-climbing algorithm
- HMMER
- Homology (biology)
- Indel
- Jalview
- List of alignment visualization software
- List of sequence alignment software
- MAFFT
- Mathematical programming
- Mixed integer programming
- Molecular phylogeny
- Multiple EM for Motif Elicitation
- MUSCLE (alignment software)
- Mutation
- Naïve algorithm
- Neighbor-joining
- NP complete
- Nucleotide
- Objective function
- PANDIT (database)
- Phylo
- Phylogenetics
- Phylogenetic tree
- Phylogeny
- Polynomial time
- Protein
- Protein domain
- Protein structure prediction
- Pseudocount
- Quantum computing
- RNA
- RNA splicing
- S. cerevisiae
- Secondary structure
- Sequence alignment
- Sequence alignment software
- Sequence motif
- Simulated annealing
- Structural alignment
- Substitution matrix
- T-Coffee
- Tertiary structure
- UGENE
- UPGMA
- Viterbi algorithm
- Yeast
- SameAs
- Aliñamento múltiple de secuencias
- Alineament múltiple de seqüències
- Alineamiento múltiple de secuencias
- Alinhamento múltiplo de sequências
- Çoklu dizi hizalaması
- m.0bgbn5
- Multiple sequence alignment
- Multiple sequence alignment
- Persejajaran sekuen jamak
- PLtR
- Poravnavanje višestrukih sekvenci
- Poravnavanje višestrukih sekvenci
- Poravnavanje višestrukih sekvenci
- Q1377767
- Множественное выравнивание последовательностей
- Множинне вирівнювання послідовностей
- تراصف السلسلة المتعدد
- همترازسازی چند توالی
- 多重序列比對
- 多重整列
- 다중서열정렬
- Subject
- Category:Bioinformatics
- Category:Computational phylogenetics
- Category:Markov models
- Thumbnail
- Url
- intro.html
- WasDerivedFrom
- Multiple sequence alignment?oldid=1117499053&ns=0
- WikiPageLength
- 52557
- Wikipage page ID
- 4066308
- Wikipage revision ID
- 1117499053
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- Template:Cite book
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