The ability to manipulate sequence, alignment, and phylogenetic tree files has become an increasingly important skill in the life sciences, whether to generate summary information or to prepare data for further downstream analysis. The command line can be an extremely powerful environment for interacting with these resources, but only if the user has the appropriate general-purpose tools on han...

INTRODUCTION Sometimes the use of a single ontology is not sufficient to cover different vocabularies for the same domain, and it becomes necessary to use several ontologies in order to encompass the entire domain knowledge and its various representations. Disciplines where this occurs include medical science and biology, as well as many of its associated subfields such as genetics, epidemiolog...

ultiple sequence alignment is one of the essential tools of studying bioinformatics. It plays an portant role in the evolution analysis and protein structure prediction. A novel method for multiple uence alignment based on wavelet package transform (MAWPT) is developed in this paper. By ans of wavelet package analysis, homologous regions can be found rapidly. Numerical examples ow that it has g...

Within machine translation, the alignment of corpora has evolved into a mature research area, aimed at providing training data for statistical or example-based machine translation systems. Moreover, the alignment information can be used for a variety of other purposes, including lexicography and the induction of tools for natural language processing. The alignment techniques used for these purp...

In most statistical machine translation systems, bilingual segments are extracted via word alignment. However, word alignment is performed independently from the requirements of the machine translation task. Furthermore, although phrase-based translation models have replacedword-based translationmodels nearly ten years ago, word-basedmodels are still widely used for word alignment. In this pape...

The application of machine learning to bioinformatics problems is well established. Less well understood is the application of bioinformatics techniques to machine learning and, in particular, the representation of non-biological data as biosequences. The aim of this paper is to explore the effects of giving amino acid representation to problematic machine learning data and to evaluate the bene...

MOTIVATION As biological inquiry produces ever more network data, such as protein-protein interaction networks, gene regulatory networks and metabolic networks, many algorithms have been proposed for the purpose of pairwise network alignment-finding a mapping from the nodes of one network to the nodes of another in such a way that the mapped nodes can be considered to correspond with respect to...

Protein data has an explosive increasing rate both in volume and diversity, yet many of its structures remain unresolved, as well their functions remain to be identified. The conventional sequence alignment tools are insufficient in remote homology detection, while the current structural alignment tools would encounter the difficulties for proteins of unresolved structure. Here, we aimed to ove...

MOTIVATION There have been several studies on the micro-inversions between human and chimpanzee, but there are large discrepancies among their results. Furthermore, all of them rely on alignment procedures or existing alignment results to identify inversions. However, the core alignment procedures do not take very small inversions into consideration. Therefore, their analyses cannot find invers...

Multiple sequence alignment has proven to be a powerful method for creating protein and DNA sequence alignment profiles. These profiles of protein families are useful tools for identifying conserved motifs, such as the catalytic triad of the serine protease family or the seven transmembrane helices of the G-protein coupled receptor family. Ultimately, the understanding of the critical motifs wi...