Fractal MapReduce decomposition of sequence alignment

Scalable Convex Multiple Sequence Alignment via Entropy-Regularized Dual Decomposition

Multiple Sequence Alignment (MSA) is one of the fundamental tasks in biological sequence analysis that underlies applications such as phylogenetic trees, profiles, and structure prediction. The task, however, is NP-hard, and the current practice resorts to heuristic and local-search methods. Recently, a convex optimization approach for MSA was proposed based on the concept of atomic norm [23], ...

Multiple Sequence Alignment Multiple Sequence Alignment

An algorithm for progressive multiple alignment of sequences with insertions " , 1. Introduction The problem of sequence alignment is to find the patterns of sequence conservation and similarity between pairs or sets of given sequences. In biological contexts, similarity between biological sequences usually amounts to either functional or structural similarities or divergence from a common ance...

Graph Optimization Using Fractal Decomposition

We introduce a method of hierarchically decomposing graph optimization problems to obtain approximate solutions with low computation. The method uses a partition on the graph to convert the original problem to a high level problem and several lower level problems. On each level, the resulting problems are in exactly the same form as the original one, so they can be further decomposed. In this w...

Sequence Alignment

Sequence Alignment

The goal of pairwise sequence alignment is to establish a correspondence between the elements in a pair of sequences that share a common property, such as common ancestry or a common structural or functional role. In computational biology, the sequences under consideration are typically nucleic acid or amino acid polymers. We will consider three variants of the pairwise sequence alignment probl...