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Title[redir]:
Automated generation of heuristics for biological sequence comparison - PMC
Description:
Exhaustive methods of sequence alignment are accurate but slow, whereas heuristic approaches run quickly, but their complexity makes them more difficult to implement. We introduce bounded sparse dynamic programming (BSDP) to allow rapid ...
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Keywords {🔍}
alignment, model, models, doi, alignments, sars, states, hsps, google, scholar, figure, hsp, pubmed, sequence, generated, bsdp, sequences, state, span, derived, genomic, search, pmc, heuristic, large, dna, upper, dynamic, system, bounds, programming, portal, sar, score, algorithms, implementation, exonerate, building, case, scores, generation, heuristics, comparison, genome, required, start, automated, article, methods, applied,
Topics {✒️}
high-scoring segment pairs [google scholar] smith [google scholar] korf references box ge license information pmcid pmc beta search large-scale genomic sequencing smith-waterman-gotoh algorithm [2 sparse dynamic programming publisher site pdf splice site prediction highest scoring parts highest scoring path optimally scoring path exhaustive dynamic programming 5 smith-waterman-gotoh smith-waterman-gotoh dynamic programming methods diagonal band surrounding trna-rrna comparisons small discrete regions finite state machines pmc disclaimer ewan birney local alignment tool linear conserved blocks finding matching words section describing automation satisfy dependency ordering compilation takes longer matching biological sequences large scale analyses large scale applications efficient string matching gapped hsp extension high score threshold ensembl cvs repository fragment chaining approaches biological sequence alignment determining optimal segmentation automata-theoretic models word-based seeding generic viterbi implementation sequence-dependent components steve searle contributed divergent loops regions nucleic acids research accommodate large gaps gapped blast excels ncbi databases
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