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The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
Align-m is a multiple sequence alignment program written by Ivo Van Walle. Align-m has the ability to accomplish the following tasks: multiple sequence alignment, include extra information to guide the sequence alignment, multiple structural alignment, homology modeling by (iteratively) combining sequence and structure alignment data,
In computer science, Hirschberg's algorithm, named after its inventor, Dan Hirschberg, is a dynamic programming algorithm that finds the optimal sequence alignment between two strings. Optimality is measured with the Levenshtein distance , defined to be the sum of the costs of insertions, replacements, deletions, and null actions needed to ...
M-Coffee: a special mode of T-Coffee that makes it possible to combine the output of the most common multiple sequence alignment packages (Muscle, ClustalW, Mafft, ProbCons, etc.). The resulting alignments are slightly better than the individual one, but most importantly the program indicates the alignment regions where the various packages ...
The algorithms then score and sort the completed phylogenetic tree, and the alignment with the maximum parsimony score is determined to be the optimal, and thus most evolutionarily likely, multiple sequence alignment. However, finding such an optimal alignment for a large number of sequences has been determined to be an NP-complete problem.
Dynamic programming is widely used in bioinformatics for tasks such as sequence alignment, protein folding, RNA structure prediction and protein-DNA binding. The first dynamic programming algorithms for protein-DNA binding were developed in the 1970s independently by Charles DeLisi in the US [ 6 ] and by Georgii Gurskii and Alexander ...
Alignment of cDNA sequences to a genome. Nucleotide DECIPHER: Alignment of rearranged genomes using 6 frame translation: Nucleotide FLAK Fuzzy whole genome alignment and analysis: Nucleotide GMAP Alignment of cDNA sequences to a genome. Identifies splice site junctions with high accuracy. Nucleotide Splign Alignment of cDNA sequences to a genome.
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.