TBtools, a Toolkit for Biologists integrating various HTS-data handling tools with a user-friendly interface

Various softwares or pipelines have been developed for biological information mining from high-throughput sequencing (HTS) data, and most of them relies on programming and command-line environment with which most biologists are unfamiliar. Bioinformatic tools with an user-friendly interface are preferred by wet-lab biologists. Here, we describe TBtools, a Toolkit for Biologists integrating various HTS-data handling tools with a user-friendly interface. It includes a large collection of functions, which facilitate many simple, routine but elaborate tasks working on HTS data, such as bulk sequence extraction, gene set functional enrichment, venn diagram and etc. TBtools can run under all operating systems with JRE1.6 and is freely available at github.com/CJ-Chen/TBtools. Since its development, it has been used by many researchers. It will be a useful toolkit for wet-lab biologists to work on all kinds of high-throughput data.

[1]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[2]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[3]  An-Yuan Guo,et al.  [GSDS: a gene structure display server]. , 2007, Yi chuan = Hereditas.

[4]  Nicholas J. Provart,et al.  An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets , 2007, PloS one.

[5]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[6]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[7]  Francesca D. Ciccarelli,et al.  FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci , 2009, Bioinform..

[8]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[9]  A. Alzohairy.  BioEdit: An important software for molecular biology , 2011 .

[10]  Jeremy D. DeBarry,et al.  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.

[11]  David G Hendrickson,et al.  Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.

[12]  Yu Xue,et al.  HemI: A Toolkit for Illustrating Heatmaps , 2014, PloS one.

[13]  Ralf Stefan Neumann,et al.  BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data , 2014, BMC Bioinformatics.

[14]  Alexander Lex,et al.  Points of view: Sets and intersections , 2014, Nature Methods.

[15]  Bo Hu,et al.  GSDS 2.0: an upgraded gene feature visualization server , 2014, Bioinform..