The Multiple Sequence Alignment Problem in Biology

Complexity of the Multiple Sequence Alignment Problem

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...

The Maximum Weight Trace Problem in Multiple Sequence Alignment

Abs t rac t . We define a new problem in multiple sequence alignment, called maximum weight trace. The problem formalizes in a natural way the common practice of merging pairwise alignments to form multiple sequence alignments, and contains a version of the minimum sum of pairs alignment problem as a special case. Informally, the input is a set of pairs of matched characters from the sequences;...

Sequence alignment in molecular biology

Molecular biology is becoming a computationally intense realm of contemporary science and faces some of the current grand scientific challenges. In its context, tools that identify, store, compare and analyze effectively large and growing numbers of bio-sequences are found of increasingly crucial importance. Biosequences are routinely compared or aligned, in a variety of ways, to infer common a...

Monte-Carlo Tree Search for the Multiple Sequence Alignment Problem

The paper considers solving the multiple sequence alignment, a combinatorial challenge in computational biology, where several DNA RNA, or protein sequences are to be arranged for high similarity. The proposal applies randomized MonteCarlo tree search with nested rollouts and is able to improve the solution quality over time. Instead of learning the position of the letters, the approach learns ...