Table 2.
Online repositories tailored for sORF identification
| Database | References | Website | Type | Description |
|---|---|---|---|---|
| sORFs.org | [14] | http://www.sorfs.org | sORF repository | Obtains experimental data from RIBO-seq with conservation analyses and rescanning MS data from PRIDE for updated small peptide validation |
| SmProt | [109] | http://bioinfo.ibp.ac.cn/SmProt/ | sORF repository | Database on small proteins specifically from lncRNA, obtains data from RIBO-seq, literature mining and MS data, integrates conservation analyses |
| OpenProt | [111, 112] | https://www.openprot.org/ | altORF resource | Contains information on protein isoforms and altORFs with experimental evidence, intergrates RIBO-seq, MS, conservation analyses and functional domains |
| ARA-PEPs | [108] | http://www.biw.kuleuven.be/CSB/ARA-PEPs | sORF repository | Repository of putative sORF-encoded peptides specifically in Arabidopsis thaliana, data obtained from in-house Tiling arrays and RNA-seq data |
| PsORF | [107] | http://psorf.whu.edu.cn/ | sORF repository | Database of sORF across different plant species, incorporating genomic, transcriptomic, RIBO-Seq and MS data |
| MetamORF | [110] | http://metamorf.hb.univ-amu.fr/ | sORF repository | A repository of unique sORFs in H. sapiens and M. musculus genomes by experimental and computational methods |
| nORFs.org | [113] | https://norfs.org/ | novel ORF (nORF) repository | Provides aggregated information from databases such as sORFs.org, OpenProt and OpenCB |
This table shows the databases available publicly for sORF identification. sORFs.org and OpenProt evaluate protein sequence identity based on BLASTp score, whereas SmProt provides a BLAST alignment search for manual evaluation of protein sequence identity. OpenProt annotates sORFs but under the label of altORFs that are longer than 30 codons and originating from ncRNAs, pseudogenes or has multiple ORFs per transcript, hence the limits set during search identification should be noted. ARA-PEPs were developed specifically from A. thaliana sORF experimental data, and PsORF aimed to store a more complete record of plant sORF. A large bulk of both MetamORF and nORFs.org data was obtained from sORFs.org and OpenProt. nORFs.org provides additional protein sequence viewer, OpenCB variants and customises annotation metrics functions