The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins
have long been and are still important issues in bioinformatics. To rapidly construct a …

This article reviews machine learning methods for bioinformatics. It presents modelling
methods, such as supervised classification, clustering and probabilistic graphical models for …

This chapter outlines several methods implemented in the MAFFT package. MAFFT is a
popular multiple sequence alignment (MSA) program with various options for the …

Multiple sequence alignment (MSA) is an important step in comparative sequence analyses.
Parallelization is a key technique for reducing the time required for large-scale sequence …

Multiple alignment of DNA sequences is an important step in various molecular biological
analyses. As a large amount of sequence data is becoming available through genome and …

Metaheuristics are the most exciting development in approximate optimization techniques of
the last two decades. They have had widespread successes in attacking a variety of difficult …

Background Unraveling the mechanisms that regulate gene expression is a major challenge
in biology. An important task in this challenge is to identify regulatory elements, especially …

The assembly of a multiple sequence alignment (MSA) has become one of the most
common tasks when dealing with sequence analysis. Unfortunately, the wide range of …

MOTIVATION: In order to increase the accuracy of multiple sequence alignments, we
designed a new strategy for optimizing multiple sequence alignments by genetic algorithm …

The enormous complexity of biological systems at the molecular level must be answered
with powerful computational methods. Computational biology is a young field, but has seen …