Pairwise Heuristic Sequence Alignment Algorithm Based on Deep Reinforcement Learning.

Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used method for comparative analysis of biological genomes. We intend to propose a novel pairwise sequence alignment method using deep reinforcement learning to break out the old pairwise alignment algorithms.

Genome classification improvements based on k-mer intervals in sequences.

Given the vast amount of genomic data, alignment-free sequence comparison methods are required due to their low computational complexity. k-mer based methods can improve comparison accuracy by extracting an effective feature of the genome sequences. The aim of this paper is to extract k-mer intervals of a sequence as a feature of a genome for high comparison accuracy.

Alignment-free sequence comparison using joint frequency and position information of k-words.

This paper proposes a novel alignment-free sequence comparison method to identify the genetic relationships of organisms with a high resolution. For an accurate comparison, both frequency and position information of k-words are obtained from genome sequences in the proposed alignment-free sequence comparison method. Using principal component analysis (PCA) and phylogeny analysis, we identify the classification performance of proposed method.

Genome-based microorganism classification using coalition formulation game.

Genome-based microorganism classification is the one of interesting issues in microorganism taxonomy. However, the advance in sequencing technology requires a low-complex algorithm to process a great amount of bio sequence data. In this paper, we suggest a coalition formation game for microorganism classification, which can be implemented in distributed manner.

Repetitive element signature-based visualization, distance computation, and classification of 1766 microbial genomes.

The genomes of living organisms are populated with pleomorphic repetitive elements (REs) of varying densities. Our hypothesis that genomic RE landscapes are species/strain/individual-specific was implemented into the Genome Signature Imaging system to visualize and compute the RE-based signatures of any genome. Following the occurrence profiling of 5-nucleotide REs/words, the information from top-50 frequency words was transformed into a genome-specific signature and visualized as Genome Signature Images (GSIs), using a CMYK scheme.

The glycosylation and in vivo stability of human granulocyte-macrophage colony-stimulating factor produced in rice cells.

Recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) has been produced in several different cell types, and has different properties depending on the production process used. There has been no report of glycosylation ratio or of the role of glycans for plant cells-derived rhGM-CSF. We investigated the terminal sialylation of rhGM-CSF produced in rice cells (rrhGM-CSF) using lectins.