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A phylogenetic tree is used to present the evolutionary relationships among the interesting biological species based on the similarities in their genetic sequences. The UPGMA is one of the popular algorithms to construct a phylogenetic tree according to the distance matrix created by the pairwise distances among taxa. To solve the performance issue of the UPGMA, the implementation of the UPGMA method...
Cloud computing, an emerging Internet-based development provides various platform and software services has become a significant issue. Many bioinformatics tools developed based on the Internet for biologists without reconstructing the whole software in the local system. Therefore, bioinformatics as a service is a new significant demand of cloud computing that integrates the bioinformatics tools to...
Proteins perform most important biochemical reactions in organisms, such as the catalysis, signal transduction, and transport of nutrients. The urgent need of automatic annotation is due to the advent of high-throughput sequencing techniques in the post-genomic era. Proteins consist of domains which are elementary building units of protein folding, function, and evolution. The evidence of protein...
Knowledge about protein–protein interactions (PPIs) unveils the molecular mechanisms of biological processes. However, the volume and content of published biomedical literature on protein interactions is expanding rapidly, making it increasingly difficult for interaction database curators to detect and curate protein interaction information manually. We present a multiple kernel learning‐based approach...
After the reference genomes of many organisms are sequenced in this post-genetic era, it has become an extremely important issue that how to do the re-sequencing and assembly for individual genomes from very large amount of reads. In this paper, we will present a re-sequencing tool designed for the Next Generation Sequencing (NGS) data. And these data are composed of a huge amount of short reads which...
Multiple sequence alignment is a scientific tool to assist the study of DNA homology, phylogeny determinations, and conserved motifs identification. Various heuristic MSA methods have been presented to obtain the resulting alignment for multiple sequences. Although these alignment tools are able to align protein, DNA, and RNA sequences successfully, they are not such successful in aligning coding...
Many new sequencing techniques have been proposed in the last few years. A number of tools have been developed for mapping short reads to the genome. However, these tools used the hash look-up table algorithm for reads or for the genome. With more and more reads sequenced and the length of reads increases; these tools will require huge memory usage and may be not practical for biologists and applications...
The classification of protein structures is essential for their function determination in bioinformatics. At present, a reasonably high rate of prediction accuracy has been achieved in classifying proteins into four classes in the SCOP database according to their primary amino acid sequences. However, for further classification into fine-grained folding categories, especially when the number of possible...
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