Table 2. Examples of Web servers and software packages developed and maintained in China.

Category	Name	Main Function	URL	Reference
Genome analysis tools	BGF	Prediction of genes in the rice genome	http://tlife.fudan.edu.cn/bgf/	[57]
	CVTree	A phylogenetic tree reconstruction tool based on whole genome sequences without alignment	http://cvtree.cbi.pku.edu.cn	[161]
	ZCURVE	A system for recognizing protein coding genes in bacterial and archaeal genomes	http://tubic.tju.edu.cn/Zcurve_B/	[5]
	Zplotter online	A program to draw and manipulate the Z curve online based on a user's input DNA sequence	http://tubic.tju.edu.cn/zcurve/	[148]
	GS-Finder	A program to find bacterial gene start sites with a self-training method	http://tubic.tju.edu.cn/GS-Finder/	[162]
	GC-Profile	A Web-based tool for visualizing and analyzing the variation of GC content in genomic sequences	http://tubic.tju.edu.cn/GC-Profile/	[163]
	FGF	A Web tool for Fishing Gene Family in a whole genome database	http://fgf.genomics.org.cn/	[164]
	BPhyOG	An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes	http://cmb.bnu.edu.cn/BPhyOG/	[165]
	SAPRED	Using new structural and sequence attributes and Support Vector Machine to predict possible disease association of single amino acid polymorphism	http://sapred.cbi.pku.edu.cn/	[82]
Expression regulation analysis tools	GBA	EST-based digital gene expression profiling	http://gba.cbi.pku.edu.cn	[166]
	CEAS	An online server to analyze transcription factor binding sites based on ChIP-chip data	http://ceas.cbi.pku.edu.cn	[99]
	OTFBS	Over-represented Transcription Factor Binding Site Prediction Tool	http://www.bioinfo.tsinghua.edu.cn/7Ezhengjsh/OTFBS/index.html	[48]
	SVAP	Identification and expression analysis of alternatively spliced isoforms	http://svap.cbi.pku.edu.cn
	CPC	Prediction of the protein-coding potential of transcripts using sequence features and support vector machine	http://cpc.cbi.pku.edu.cn	[107]
	RDfolder	A Web server for prediction of RNA secondary structure	http://rna.cbi.pku.edu.cn	[108]
	miRAS	A data processing system for miRNA expression profiling study	http://e-science.tsinghua.edu.cn/miras/	[106]
	MiPred	Classification of real and pseudo microRNA precursors using random forest prediction model with combined features	http://www.bioinf.seu.edu.cn/miRNA/	[103]
	RFRCDB-siRNA	Improved design of siRNAs by random forest regression model coupled with database searching	http://www.bioinf.seu.edu.cn/siRNA/index.htm	[167]
Protein analysis tools	EasyGO	Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species	http://bioinformatics.cau.edu.cn/easygo/	[168]
	CTKPred	An SVM-based method for the prediction and classification of the cytokine superfamily	http://www.bioinfo.tsinghua.edu.cn/7Ehn/CTKPred/index.html	[169]
	GNBSL	A new integrative system to predict the subcellular location for Gram-negative bacteria proteins	http://166.111.24.5/webtools/GNBSL/index.htm	[127]
	MeMo	A Web tool for prediction of protein methylation modifications	http://www.bioinfo.tsinghua.edu.cn/∼tigerchen/memo/contact.html	[170]
	KOBAS	A Web-based platform for pathway identification	http://kobas.cbi.pku.edu.cn	[171]
	IntNetDB	An integrated protein–protein interaction network database generated by a probabilistic model	http://hanlab.genetics.ac.cn/IntNetDB.htm	[172]
Platforms	BOD	A customizable bioinformatics on demand system accommodating multiple steps and parallel tasks	http://e-science.tsinghua.edu.cn/bod/index.jsp	[173]
	ABCGrid	Application for Bioinformatics Computing Grid	http://abcgrid.cbi.pku.edu.cn	[174]