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Optimal sequence alignment allowing for long gaps

โœ Scribed by Osamu Gotoh


Book ID
112753769
Publisher
Springer
Year
1990
Tongue
English
Weight
775 KB
Volume
52
Category
Article
ISSN
1522-9602

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Optimal sequence alignment allowing for
โœ Osamu Gotoh ๐Ÿ“‚ Article ๐Ÿ“… 1990 ๐Ÿ› Springer ๐ŸŒ English โš– 735 KB

A new algorithm for optimal sequence alignment allowing for long insertions and deletions is developed. The algorithm requires O((L+C)MN) computational steps, O(LN) primary memory and O(MN) secondary memory storage, where M and N (M~> N) are sequence lengths, L (typically L~< 3) is the number of seg

Normalization of Affine Gap Costs Used i
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It is shown how to normalize the costs of an alignment algorithm that employs affine or linear gap costs. The normalized costs are interpreted as the -log probabilities of the instructions of a finite-state edit-machine. This gives an explicit model relating sequences that can be linked to processes

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โœ DAVID R. POWELL; LLOYD ALLISON; TREVOR I. DIX ๐Ÿ“‚ Article ๐Ÿ“… 2000 ๐Ÿ› Elsevier Science ๐ŸŒ English โš– 160 KB

Alignment algorithms can be used to infer a relationship between sequences when the true relationship is unknown. Simple alignment algorithms use a cost function that gives a "xed cost to each possible point mutation\*mismatch, deletion, insertion. These algorithms tend to "nd optimal alignments tha

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โœ Stephen F. Altschul ๐Ÿ“‚ Article ๐Ÿ“… 1998 ๐Ÿ› John Wiley and Sons ๐ŸŒ English โš– 125 KB

Based on the observation that a single mutational event can delete or insert multiple residues, affine gap costs for sequence alignment charge a penalty for the existence of a gap, and a further length-dependent penalty. From structural or multiple alignments of distantly related proteins, it has be