TABLE 4.
Commonly used databases for micropeptide research.
| Name | Characteristics | Website | References |
|---|---|---|---|
| BLAST | A tool for similarity analysis in protein databases or gene databases to find sequences that are similar to the query sequence. This includes patterns such as blastp, blastx, etc | https://blast.ncbi.nlm.nih.gov/Blast.cgi | Sayers et al. (2021) |
| Pfam | A database that classifies protein sequences into families and domains, which can be queried for protein conserved structural domains | http://pfam.xfam.org/ | Mistry et al. (2021) |
| CDD | NCBI conserved domain database, annotated biomolecular sequences with evolutionarily conserved protein domain footprint positions, as well as functional sites deduced from these footprints | https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml | Lu et al. (2020) |
| cncRNADB | Manually manage a resource database of bifunctional RNA (cncRNA) with protein-coding and non-coding functions | http://www.rna-society.org/cncrnadb/ | Huang et al. (2021) |
| LNCipedia | A public database for storing lncRNA sequences and annotation information | https://lncipedia.org/ | Volders et al. (2019) |
| lnCAR | A comprehensive resource for lncRNA from cancer arrays (including lncRNA coding information) | https://lncar.renlab.org/ | Zheng et al. (2019) |
| NONCODE | A database annotated with a large amount of lncRNA information | http://www.noncode.org/ | Zhao et al. (2016) |
| UCSC | Genome Browser database that provides high quality visualization of genomic data and genome annotation. Has tools such as BLAT, track hubs, etc. for viewing, analyzing and downloading data | https://genome.ucsc.edu | Navarro Gonzalez et al. (2021) |
| UniProt | The most comprehensive database of protein sequence and annotation information, consisting of UniProtKB, UniRef, and UniParc, and integrating data from three major databases, swiss-prot, TrEMBL, and PIR-PSD | https://www.uniprot.org/ | UniProt, (2021) |
| Expasy | A database of reliable and most advanced bioinformatics service tools and resources is stored. Has tools such as protscale, TMpred, etc. for viewing, analyzing, and downloading data | https://www.expasy.org/ | Duvaud et al. (2021) |
| LncPep | The lncRNA coding peptides database | http://www.shenglilabs.com/LncPep/ | Liu et al. (2022) |
| SPENCER | A comprehensive database for small peptides encoded by noncoding RNAs in cancer patients | http://spencer.renlab.org | Luo et al. (2022) |