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Due to the rapid increase in biological data dimension and acquisition rate, the traditional analysis methods are unable to achieve acceptable accuracy. Recently, Deep learning technologies have shown outstanding results in many domains; especially in pattern recognition in the field of bioinformatics. In this paper, we provide background of what deep learning and its frameworks. In addition, we review...
In the 21st century, antibiotic resistance has become a crucial and growing phenomenon in contemporary medicine. Multidrug resistant leads that antibiotics cannot be used to treat infections. In this paper, we propose a novel and efficient method to identify drug resistance genes from raw reads produced by next generation sequencing technology for metagenomes. The experimental results show that the...
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...
The importance of detecting and subtyping human papillomaviruses (HPVs) in clinical and epidemiological studies has been well addressed. In detecting the most common types of HPV, type 16 (HPV-16) and type 18 (HPV-18), in the cervical mucous of patients in a simple and rapid manner, the assay of a label- free colorimetric DNA sensing method based on sequence sandwich hybridization with oligonucleotide-functionalized...
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