منابع مشابه
Constrained sequence alignment.
This paper presents a dynamic programming algorithm for aligning two sequences when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires only O(F) computations time and O(M+N) space, when F is the area of the feasible region and M and N are the sequence lengths. The result extends to concave ...
متن کاملOne-Annotated Constrained Sequence Alignment
The constrained multiple sequence alignment (CMSA) problem is to align a set of strings such that the given patterns (the constraint) appear in the same positions in a specified order in each of the strings in the resulting alignment. The best previous result for the pair-wise version takes O(mn) time and space [2, 10], where m is the number of patterns (defined later) and n is the maximum stri...
متن کاملRegular Expression Constrained Sequence Alignment
Given strings S1, S2, and a regular expression R, we introduce regular expression constrained sequence alignment as the problem of finding the maximum alignment score between S1 and S2 over all alignments such that in these alignments there exists a segment where some substring s1 of S1 is aligned with some substring s2 of S2, and both s1 and s2 match R, i.e. s1, s2 ∈ L(R) where L(R) is the reg...
متن کاملCSA-X: Modularized Constrained Multiple Sequence Alignment
Imposing additional constraints on multiple sequence alignment (MSA) algorithms can often produce more biologically meaningful alignments. Hence, various constrained multiple sequence alignment (CMSA) algorithms have been developed in the literature, where researchers used anchor points, regular expressions, or context-free-grammars to specify the constraints, wherein alignments produced are fo...
متن کاملRegular Language Constrained Sequence Alignment Revisited
Imposing constraints in the form of a finite automaton or a regular expression is an effective way to incorporate additional a priori knowledge into sequence alignment procedures. With this motivation, the Regular Expression Constrained Sequence Alignment Problem was introduced, which proposed an O(n²t⁴) time and O(n²t²) space algorithm for solving it, where n is the length of the input strings...
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ژورنال
عنوان ژورنال: Bulletin of Mathematical Biology
سال: 1993
ISSN: 0092-8240
DOI: 10.1016/s0092-8240(05)80237-x