نتایج جستجو برای: homology search
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Dynamic programming [1] has full sensitivity, but too slow for large scale homology search. FASTA / BLAST type of heuristics [2] trade sensitivity for speed. Can we have both sensitivity and speed? We present the mathematical theory of optimized spaced seeds which allows modern homology search to achieve high sensitivity and high speed simultaneously. The spaced seed methodology is implemented ...
MOTIVATION Life science researchers often require an exhaustive list of protein coding genes similar to a given query gene. To find such genes, homology search tools, such as BLAST or PatternHunter, return a set of high-scoring pairs (HSPs). These HSPs then need to be correlated with existing sequence annotations, or assembled manually into putative gene structures. This process is error-prone ...
Homology search methods have advanced substantially in recent years. Beginning with the elegant Needleman-Wunsch and Smith-Waterman dynamic programming techiques of the 1970s, algorithms have been developed that were appropriate for the data sets and computer systems of their times. As data sets grew, faster but less sensitive heuristic algorithms, such as FASTA and BLAST, became a dominant for...
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