MOTIVATION: Metagenomic approaches hold the potential to characterize microbial communities and unravel the intricate link between the microbiome and biological processes. Assembly is one of the most critical steps in metagenomics experiments. It con...
BACKGROUND: Prokaryotic viruses referred to as phages can be divided into virulent and temperate phages. Distinguishing virulent and temperate phage-derived sequences in metavirome data is important for elucidating their different roles in interactio...
Identification of prokaryotic transposases (Tnps) not only gives insight into the spread of antibiotic resistance and virulence but the process of DNA movement. This study aimed to develop a classifier for predicting Tnps in bacteria and archaea usin...
SUMMARY: We present the first tool of gene prediction, PlasGUN, for plasmid metagenomic short-read data. The tool, developed based on deep learning algorithm of multiple input Convolutional Neural Network, demonstrates much better performance when te...
MOTIVATION: Almost all protein residue contact prediction methods rely on the availability of deep multiple sequence alignments (MSAs). However, many proteins from the poorly populated families do not have sufficient number of homologs in the convent...
IEEE/ACM transactions on computational biology and bioinformatics
Jan 1, 2020
The recent advent of Metagenome Wide Association Studies (MGWAS) provides insight into the role of microbes on human health and disease. However, the studies present several computational challenges. In this paper, we demonstrate a novel, efficient, ...
MOTIVATION: When analyzing viral metagenomic sequences, it is often desired to filter the results of a BLAST analysis by the host species of the virus. VHost-Classifier automates this procedure using a natural language processing algorithm written in...
BACKGROUND: Phages and plasmids are the major components of mobile genetic elements, and fragments from such elements generally co-exist with chromosome-derived fragments in sequenced metagenomic data. However, there is a lack of efficient methods th...