The BLAST-2.9.1+ program was embedded in the NHCCDB database with a user-friendly graphic interface to help users search similarity sequences. A total of 9 species genomic data including 21 datasets contained in the BLAST+ database. Users can upload or paste FASTA format sequences (Amino acid or nucleotide acid sequences) according to the research aims. E-value and output parameters can be modified or set to the default values before performing blastp, blastn, blastx, tblastn or tblastx program to find similarity sequences. The results page will provide when users submit BLAST+ search, and users can download or browse BLAST+ results. Last but not least, we also provide a BLAST+ result ID, and users can browse their result within seven days by using Tools Result Search function search result ID.

This function can be used for Pfam annotation. Datasets is Pfam 33.1. You can download datasets from Pfam database. We provide a graphic interface based on HTML5. FASTA format amino acid sequences can be directly submitted by uploading a FASTA file or paste the data to the data frame. According to the demand, users can set a e-value to search against Pfam datasets. The result page will provide browse and download link after users submit Pfam search. And users can browse results by using Tools Result Search function search Pfam result ID.

We present Synteny Finder, a user-friendly online synteny analysis function, which we build using BLAST-2.9.1+ , MCscanX and Perl and Java scripts. Users can upload reference and query gene sequences with FASTA format and gene structure file to Synteny Finder tools. Two parameters, including BLAST e-value and MCscanX gap can be adjust according to your aim. After you click submit button, MCscanX analysis results can be browse and download according the link provided in the results interface. And analysis id present in the results page that you can browse and download this results by searching id using Tools Results Search tools. We also provide visualize synteny finder results function build by Java scripts, which you can select visualization parameters in the results page. Mainly including circle, dual, dot and bar plot four types. Users can according to their aim to set width and height parameters. Visualization results output format support pdf, png, svg, jpeg, eps and bmp six format types, and users can download visualization results.

According to eggnog annotation, we build the graphic interface of GO Enrichment tools by using R scripts. Now, GO Enrichment tools support forty kinds of protein data (different subspecies, cultivate and version protein data). Users can submitted "Interest gene List" by copying data to the frame. Some enrichment parameters, such as p-value correction method, p value and q value can be set up according to research aims. Enrichment result can be visual with barplot, dotplot, centplot, emapplot and heatplot five types. Users can adjust visualization parameters according the enrichment results. In the result page, users can adjust the size and download the PDF format visualization results. And we also provide browse and download enrichment data in result page. Users can browse enrichment results by searching results id provided in results page using Tools Result Search function.

According to eggnog annotation, we build the graphic interface of KEGG Enrichment tools by using R scripts. Now, KEGG Enrichment tools support forty kinds of protein data (different subspecies, cultivate and version protein data). Users can submitted "Interest gene List" by copying data to the frame. Some enrichment parameters, such as p-value correction method, p value and q value can be set up according to research aims. Enrichment result can be visual with barplot, dotplot, centplot, emapplot and heatplot five types. Users can adjust visualization parameters according the enrichment results. In the result page, users can adjust the size and download the PDF format visualization results. And we also provide browse and download enrichment data in result page. Users can browse enrichment results by searching results id provided in results page using Tools Result Search function.

Motif Discovery tools build by MEME program. Motif Discovery discovers novel, ungapped motifs in your sequences. And Motif Discovery splits variable-length patterns into two or more separate motifs.

Primer 3.0 program was embedded in the NHCCDB with a user-friendly graphic interface. Nucleotide acid sequences can be directly submitted by pasting the sequence to the frame. Same parameters, such as task, primer size, primer TM, primer GC%, product TM, product size, max 3’ stability and primer number. Users can modify the parameters according to research demand. But we suggest users simply set to the default parameter values.

SSR commonly used genetic marker system in plant genetics and breeding. MISA program download from MISA database (a web server for microsatellite prediction) used to set up SSR Finder tools. This function used to identify SSR in the genome sequence and design three pairs of primers. Pasting nucleotide acid sequences or uploading sequences with a FASTA format to submit users data. Users can download or browse identify results, and browse results using Tools Results Search tools searching results id.

In NHCCDB, we have incorporated a genome browser (JBrowse), developed using HTML5 and JavaScript. JBrowse can be used to browse and view the genome sequences and gene modules. At the moment, this function supports 23 genome datasets. JBrowse supports visualization scaling and smooth transition from the genome level to nucleotide base level. Furthermore, JBrowse supports the query of the genomic sequences at the individual chromosome level. Users can click on gene modules to view gene information such as names, positions, types, lengths, and sequences. This function also supports the download of gene sequences.