Sweetpotato Germplasm and Genome Resource Database

The Tools module provides five tools for sweetpotato genomics research: BLAST sequence similarity search, Cas9 Design for genome-aware sgRNA selection, Primer Designer for PCR primer design, Enrichment Analysis for GO/KEGG functional enrichment, and Sequence Fetch for reference sequence extraction.

Sequence similarity searches against genome, CDS, and protein databases for all 10 supported assemblies. Five BLAST programs are supported: blastn (nucleotide vs nucleotide), blastp (protein vs protein), blastx (translated nucleotide vs protein), tblastn (protein vs translated nucleotide), and tblastx (translated vs translated). Users input a query sequence in FASTA format, select the target database and species, and receive a tabular result with alignment score, E-value, identity percentage, and genome browser links for each hit.

A genome-aware SpCas9 sgRNA design and exact-match inspection workbench covering six assemblies: Beauregard v4, Xushu 18 / IBA r1.0, pasi3, Mx23Hm / Itr r2.2, NSP306 v3, and NSP323 v3. Users can define a target by Gene ID or a 1-based genomic interval, filter candidates by annotation, GC content, and genome-wide exact hit count, then download the ranked results. A third query mode checks an existing 20 nt sgRNA against the selected genome. The precomputed NGG indexes contain 173,776,174 unique guides and 270,774,833 PAM-valid genomic sites and are queried through read-only NumPy memory maps.

An integrated primer design tool for designing PCR and sequencing primers. Users provide a target nucleotide sequence; the tool automatically predicts optimal primer pairs with melting temperature (Tm), GC content, amplicon size, and hairpin/dimer checks. Results include all candidate primer pairs ranked by quality score.

Gene Ontology (GO) and KEGG pathway over-representation analysis for user-provided gene lists. Analysis uses gseapy with Fisher's exact test and Benjamini–Hochberg FDR correction. Species-specific background gene sets (GMT format) are pre-computed from genome-wide functional annotation for seven organisms: Beauregard, New Kawogo, Tanzania, Taizhong 6, I. trifida, I. triloba, and Xushu 18. Significantly enriched terms (adjusted p < 0.05) are reported with gene counts and visualized as interactive bar and dot charts.

Extract reference sequence from a supported assembly by genomic interval (contig, start, end; up to 5 Mb) or by gene ID. Gene mode accepts upstream and downstream flanks of up to 1 Mb each, and either mode can return the reverse complement. Results can be copied or downloaded as FASTA.