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In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. [1] Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix.
Recent development has focused on improving the time and space cost of the algorithm while maintaining quality. For example, in 2013, a Fast Optimal Global Sequence Alignment Algorithm (FOGSAA), [9] suggested alignment of nucleotide/protein sequences faster than other optimal global alignment methods, including the Needleman–Wunsch algorithm ...
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.
Combines DNA and Protein alignment, by back translating the protein alignment to DNA. DNA/Protein (special) Local or global: Wernersson and Pedersen: 2003 (newest version 2005) SAGA Sequence alignment by genetic algorithm: Protein: Local or global: C. Notredame et al. 1996 (new version 1998) SAM Hidden Markov model: Protein: Local or global: A ...
BLAT can be used to align DNA sequences as well as protein and translated nucleotide (mRNA or DNA) sequences. It is designed to work best on sequences with great similarity. The DNA search is most effective for primates and the protein search is effective for land vertebrates.
In computational phylogenetics, tree alignment is a computational problem concerned with producing multiple sequence alignments, or alignments of three or more sequences of DNA, RNA, or protein. Sequences are arranged into a phylogenetic tree , modeling the evolutionary relationships between species or taxa .
Fast statistical alignment or FSA is a multiple sequence alignment program for aligning many proteins, RNAs, or long genomic DNA sequences. Along with MUSCLE and MAFFT, FSA is one of the few sequence alignment programs which can align datasets of hundreds or thousands of sequences. FSA uses a different optimization criterion which allows it to ...
Sequence alignment can also reveal conserved domains and motifs. One motivation for local alignment is the difficulty of obtaining correct alignments in regions of low similarity between distantly related biological sequences, because mutations have added too much 'noise' over evolutionary time to allow for a meaningful comparison of those regions.