RiboToolkit, a convenient, freely available, web-based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs.
PRFdb (v2.0) is a database which currently hosts 2884 Ribo-seq datasets from 293 studies, covering 29 different species. In line with the significant expansion of Ribo-seq data available in the database, RPFdb v2.0 includes a refined analysis pipeline with multi-step quality control applied for improving the pre-processing and alignment of Ribo-seq data, new functional modules providing actively translated ORFs information, and more web features for better database usability.
TranslatomeDB is a comprehensive database which provides collection and integrated analysis of published and user-generated translatome sequencing data. It includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels.
The Ribosomal Protein Gene Database is dedicated to collecting and organizing information related to ribosomal protein genes. Its main purposes include providing basic information about ribosomal protein genes, such as gene sequences and protein structures, collecting information on ribosomal protein genes from different species for comparative analysis, facilitating the analysis of ribosomal protein gene families and evolutionary relationships for researchers, and providing foundational data support for studying the functions of ribosomes and translation regulation in biological processes.
SmProt contains records of Small Proteins encoded by genes, especially for ones from UTRs and non-coding RNAs. The selected small proteins were identified from ribosome profiling data, literature, mass spectrometry (MS), etc., carried out in eight species including Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Saccharomyces cerevisiae, Caenorhabditis elegans and Escherichia coli. Moreover, SmProt contains features for the collected small proteins on their sequences, genomic locations, tissues/cell lines, assessment reflecting coding potential, function, variants, and related diseases that have been verified or predicted, etc.
RibORF is a computational pipeline to systematically identify translated open reading frames (ORFs), based on read distribution features representing active translation, including 3-nt periodicity and uniformness across codons.
Ribo TIS Hunter (Ribo-TISH) is used for identifying translation activities using ribosome profiling data. Ribo-TISH uses statistical tests to assess the significance of translation activities. It captures significant TISs using negative binomial test, and frame biased open reading frames (ORFs) using rank sum test. Ribo-TISH can also perform differential analysis between two TI-Seq data.
Plastid is a versatile toolkit that has been used to analyze data from multiple NGS assays, including RNA-seq, ribosome profiling, and DMS-seq. It forms the genomic engine of our ORF annotation tool, ORF-RATER, and is readily adapted to novel NGS assays.
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.
RiboVIEW is developed to perform robust quality control of ribosome profiling data (RiboQC), to efficiently visualize ribosome positions and to estimate ribosome speed (RiboMine) in an unbiased way. It contains an R pipeline to setup and undertake the analyses that offers the user an HTML page to scan own data regarding the following aspects: periodicity, ligation and digestion of footprints; reproducibility and batch effects of replicates; drug-related artifacts; unbiased codon enrichment including variability between mRNAs, for A, P and E sites; mining of some causal or confounding factors.