Constrained sequence alignment.
نویسندگان
چکیده
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 gap penalities, with somewhat increased time and space bounds.
منابع مشابه
An Algorithm and Applications to Sequence Alignment with Weighted Constraints
Given two sequences S1, S2, and a constrained sequence C, a longest common subsequence of S1, S2 with restriction to C is called a constrained longest common subsequence of S1 and S2 with C. At the same time, an optimal alignment of S1, S2 with restriction to C is called a constrained pairwise sequence alignment of S1 and S2 with C. Previous algorithms have shown that the constrained longest co...
متن کاملA simple algorithm for the constrained sequence problems
In this paper we address the constrained longest common subsequence problem. Given two sequences X , Y and a constrained sequence P , a sequence Z is a constrained longest common subsequence for X and Y with respect to P if Z is the longest subsequence of X and Y such that P is a subsequence of Z. Recently, Tsai [7] proposed an O(n ·m · r) time algorithm to solve this problem using dynamic prog...
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 کاملAn Application of the ABS LX Algorithm to Multiple Sequence Alignment
We present an application of ABS algorithms for multiple sequence alignment (MSA). The Markov decision process (MDP) based model leads to a linear programming problem (LPP), whose solution is linked to a suggested alignment. The important features of our work include the facility of alignment of multiple sequences simultaneously and no limit for the length of the sequences. Our goal here is to ...
متن کاملFastPCMSA: An Improved Parallel Algorithm for the Constrained Multiple Sequence Alignment Problem
The constrained multiple sequence alignment (CMSA) problem is to align given sequences S1, S2, ..., Sn to maximize a similarity score with the constraint that P is “contained” in the resulting alignment. The CMSA problem can be considered as a constrained path search problem in the dynamic programming matrix. The problem has a dynamic programming solution that requires O(2|S1||S2|...|Sn||P |) t...
متن کاملA memory-efficient algorithm for multiple sequence alignment with constraints
MOTIVATION Recently, the concept of the constrained sequence alignment was proposed to incorporate the knowledge of biologists about structures/functionalities/consensuses of their datasets into sequence alignment such that the user-specified residues/nucleotides are aligned together in the computed alignment. The currently developed programs use the so-called progressive approach to efficientl...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Bulletin of mathematical biology
دوره 55 3 شماره
صفحات -
تاریخ انتشار 1993