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Alignment preserving non-heuristic: Both: Local or global: S.H. Sze, Y. Lu, Q. Yang. 2006: RevTrans 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 ...
Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context. The Smith–Waterman algorithm is a general local alignment method based on the same dynamic programming scheme but with additional choices to start and end at any place. [4]
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.
In bioinformatics, the BLOSUM (BLOcks SUbstitution Matrix) matrix is a substitution matrix used for sequence alignment of proteins. BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences. They are based on local alignments. BLOSUM matrices were first introduced in a paper by Steven Henikoff and Jorja ...
In bioinformatics, BLAST (basic local alignment search tool) [3] is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA 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 the sequences in each query set. Multiple alignments are often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related.
The extensible NEXUS file format is widely used in phylogenetics, evolutionary biology, and bioinformatics.It stores information about taxa, morphological character states, DNA and protein sequence alignments, distances, and phylogenetic trees. [1]
In bioinformatics, a spaced seed is a pattern of relevant and irrelevant positions in a biosequence and a method of approximate string matching that allows for substitutions. They are a straightforward modification to the earliest heuristic -based alignment efforts that allow for minor differences between the sequences of interest.