Bioinformatic Tools(software, database, and online server)
PGAP: Pan-Genomes Analysis Pipeline PGAP is a pan-genome analysis pipeline (PGAP), which can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters (Zhao et al, Bioinformatics, 2012).
PanGP is a tool for quickly analyzing bacterial pan-genome profile. It has integrated two kinds of sample algorithm, totally random (TR) and distance guide (DG), so that it could calculate the pan-genome profile of a population with dozens of or hundreds of strains at extremely low time-cost (Zhao et al, Bioinformatics, 2014).
PGAP-X: Extension on pan-genome analysis pipeline
PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different conservative levels, and genetic variation from pan-genome sight (Zhao et al, BMC Genomics, 2018).
sgRNA online is an online tool that identifies efficient sgRNAs for CRISPR editing of mouse and human genomes. It supports both classic Cas9 and xCa9 3.7.
NucMap is a database of genome-wide nucleosome positioning map across species. It is dedicated to collecting, analyzing and storing nucleosome positioning data in all organisms. NucMap provides services on querying and visualizing nucleosome positioning information at single nucleotide resolution. Meanwhile, it also provides some enrichment analysis on interested genes or samples (Zhao et al, Nucleic Acids Research, 2018).
TFSyntax is an open access and comprehensive database of transcription factors (TFs) binding syntax in mammalian genomes. It mainly focuses on the rules how TFs bind to enhancers with the context of other partners and how TFs cooperate with each other (Zhao, Nucleic Acids Research, 2023).