Multiple sequence alignment with user-defined constraints at GOBICS

Abstract

Most multi-alignment methods are fully automated, i.e. they are based on a fixed set of mathematical rules. For various reasons, such methods may fail to produce biologically meaningful alignments. Herein, we describe a semi-automatic approach to multiple sequence alignment where biological expert knowledge can be used to influence the alignment procedure. The user can specify parts of the sequences that are biologically related to each other; our software program uses these sites as anchor points and creates a multiple alignment respecting these user-defined constraints. By using known functionally, structurally or evolutionarily related positions of the input sequences as anchor points, our method can produce alignments that reflect the true biological relationships among the input sequences more accurately than fully automated procedures can do.

BDD-Constrained A^* Search: A Fast Method for Solving Constrained Shortest-Path Problems

“…Therefore, we prepared 10 instances for each setting. We compared the proposed method with Yamada02 [2], a dedicated algorithm for DCKP that uses Lagrangian relaxation and the branch and bound method.…”

“…In the same way, we can solve constrained version of these combinatorial optimization problems via CDSP. These include problems of practical importance such as the 0-1 knapsack problem with disjunctive constraints [1], sequence alignment with user-defined anchor points [2], and incorporating knowledge based constraints into statistical machine learning models [3].…”

Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination

“…Recently discussed constrained alignment approaches handled constraints like precedence constraints [16] and anchor constraints [15]. Such constraints can be encoded in our model straightforwardly and are handled by restricting the domains of variables, which even increases the efficiency of our algorithm.…”

“…Anchors An anchor constraint, as discussed in [15], tells that position i in the first sequence and position j in the second sequence can only be aligned to each other and furthermore, positions strictly left (resp. right) of i are aligned to positions strictly left (resp.…”

“…Only for certain special constraints, alignment algorithms have been discussed. In particular, there are approaches that incorporate anchor constraints [15] and precedence constraints [16]. We will later discuss how such constraints fit into our newly introduced framework as simple cases.…”