Comprehensive overview of data resources, annotations, and analytical tools available in CnidoSite database.
| Class/Order/Family/Speices | 7/22/107/325 |
|---|---|
| Assembled Genomes With Full Annotation | 145 |
| Tracks in JBrowse | 3,141 |
| Paleobiological Records | 410 |
| Busco genes | 542,399 |
| Protein-Coding Genes | 5,450,036 |
| Mitogenomic Datasets | 78 |
| Transcriptomic Datasets | 15,642 |
| Sing-cell RNA-seq Datasets | 33 |
| Proteomic Datasets | 46 |
| Epigenomic Datasets | 723 |
| Metagenomic Datasets | 1,650 |
| Phenotype Datasets | 151,046 |
| Mitochondrial Datasets | 146 |
| Co-Expressed Networks/Gene Pairs | 31/13,793,211 |
| Cell types | 206 |
| Cell markers | 297,645 |
| Quantified Proteins | 83,306 |
| Epigenetic Modification Type/Peaks | 13/739,820,475 |
| Metagenome-Assembled Genomes | 315 |
| NR/Uniprot/GO/KEGG/Pfam/Panther/Interpro annotation | 89,363,242/140,368,972/36,073,035/1,362,980/7,479,863/3,805,615/35,694,300 |
| TFs/Ubiquitin families | 96,854/306,859 |
| Orthologous Families | 3,621,064 |
| Module | Software | Parameter | Links |
|---|---|---|---|
| Fossil records | PBDB | default | https://paleobiodb.org/#/ |
| Gene annotation | InterProScan v.5.67-97.0 | -f tsv -goterms -pa | https://github.com/ebi-pf-team/interproscan |
| Busco Gene | BUSCO v.5.8.2 | -l metazoa_odb12 -m proteins | https://gitlab.com/ezlab/busco |
| Transposable Elements | RepeatModeler v.2.0.7 RepeatModeler v.4.2.1 | -engine rmblast -LTRStruct -gff -e rmblast -nolow | https://github.com/Dfam-consortium/RepeatModeler https://github.com/Dfam-consortium/RepeatMasker |
| TFs/Ubs | HMMER v.3.4 | cut-off: 0.0001 | http://hmmer.org/ |
| Gene Family | OrthoFinder v.2.5.5 | default | https://github.com/davidemms/OrthoFinder |
| Pan-geneset | Count | Wagner_parsimony -gain 1 -max_paralogs 200 Posteriors -max_paralogs 200 | https://www.iro.umontreal.ca/~csuros/gene_content/count.html |
| Mitogenomic Datasets | OGDRAW v.1.3.1 | default | https://chlorobox.mpimp-golm.mpg.de/OGDraw.html |
| Proteomic Datasets | Blastp | default | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| Epigenomic Datasets | MACS3 | default | https://github.com/macs3-project/MACS |
| Co-expression network | Cytoscape v3.10.3 | default | https://cytoscape.org/ |
| Single-cell Datasets | Seurat v4.4 | LogNormalize | https://satijalab.org/seurat |
| Species tree | phylotree | default | https://www.phylotree.org/ |
| Primer Design | Primer3Plus | default | https://github.com/primer3-org |
| Database construction | LAMP | default | https://github.com/teddysun/lamp |
