منابع مشابه
Reduced space sequence alignment
MOTIVATION Sequence alignment is the problem of finding the optimal character-by-character correspondence between two sequences. It can be readily solved in O(n2) time and O(n2) space on a serial machine, or in O(n) time with O(n) space per O(n) processing elements on a parallel machine. Hirschberg's divide-and-conquer approach for finding the single best path reduces space use by a factor of n...
متن کاملOptimizing reduced-space sequence analysis
MOTIVATION Dynamic programming is the core algorithm of sequence comparison, alignment and linear hidden Markov model (HMM) training. For a pair of sequence lengths m and n, the problem can be solved readily in O(mn)time and O(mn)space. The checkpoint algorithm introduced by Grice et al. (CABIOS, 13, 45--53, 1997) runs in O(Lmn)time and O(Lm(L) square root of n)space, where L is a positive inte...
متن کاملMultiple sequence alignment by conformational space annealing.
We present a new method for multiple sequence alignment (MSA), which we call MSACSA. The method is based on the direct application of a global optimization method called the conformational space annealing (CSA) to a consistency-based score function constructed from pairwise sequence alignments between constituting sequences. We applied MSACSA to two MSA databases, the 82 families from the BAliB...
متن کاملParallel Three-sequence Alignment with Space-efficient
The sequence alignment is a fundamental problem in computational biology. Many sequence alignment methods have been proposed, such as pair-wise sequence alignment, multiple sequence alignment (MSA), syntenic alignment, constraint multiple sequence alignment, and etc. Among them, pair-wise sequence alignment is a most commonly used method. Recently, MSA is more and more important which has been ...
متن کاملParallel Sequence Alignment in Limited Space
Sequence comparison with affine gap costs is a problem that is readily parallelizable on simple single-instruction, multiple-data stream (SIMD) parallel processors using only constant space per processing element. Unfortunately, the twin problem of sequence alignment, finding the optimal character-by-character correspondence between two sequences, is more complicated. While the innovative O(n2)...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 1997
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/13.1.45