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GWIPS-viz / Genome Wide Information on Protein Synthesis visualized
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Provides access to the genomic alignments of public ribo-seq reads in conjunction with mRNA-seq reads along with relevant annotation tracks. GWIPS-viz is a specialized ribo-seq browser allowing researchers to support ribo-seq evidence for alternative proteoforms inferred from phylogenetic analysis or detect with proteomics or other experimental techniques. It can be used as a support tool for predictions based on other approaches and for generating hypotheses that can be tested using methods other than ribo-seq.
sORFs.org
Allows to identify short open reading frames (sORFS). SORFS.org presents two interfaces: (1) the default query interface provides real-time lookup of sORFs with limited query possibilities and (2) a BioMart query interface was developed enabling advanced query and export options. This database contains more than 260 000 sORFs. This detail page also contains a RIBO-seq visualization tool, permitting manual inspection of RIBOseq data. This extensive platform can help researchers with limited bioinformatics knowledge in sORFS domain.
RPFdb
A comprehensive resource for hosting, analyzing and visualizing ribosome protected mRNA fragment (RPF) data. RPFdb contains 777 samples from 82 studies in 8 species, processed and reanalyzed by a unified pipeline. There are two ways to query the database: by keywords of studies or by genes. The outputs are presented in three levels. (i) Study level: including meta information of studies and reprocessed data for gene expression of translated mRNAs; (ii) Sample level: including global perspective of translated mRNA and a list of the most translated mRNA of each sample from a study; (iii) Gene level: including normalized sequence counts of translated mRNA on different genomic location of a gene from multiple samples and studies. To explore rich information provided by RPF, RPFdb also provides a genome browser to query and visualize context-specific translated mRNA.
SmProt / Small Proteins database
Contains several information about small proteins. SmProt is a database that provides a user-friendly website for users to submit, browse, search, blast, download or export data about small proteins. This database includes a service for the BLAST alignment search and an integrated local UCSC Genome Browser service (allowing the visualization of the genomic locations of small proteins). It predicts the functions of the small proteins curated from ribosome profiling calculation and literature mining and describes a high confidence set of small proteins.
HSPVdb / Human Short Peptide Variation Database
Provides peptides derived from genomic sequence variations. HSPVdb is a database, fully dedicated to find polymorphic epitopes, that only contains peptides of seven amino acids or longer. This resource permits the identification of published polymorphic single-nucleotide polymorphism (SNP) and/or alternative reading frames (ARFs)-derived epitopes from a mass spectrometry-based proteomics workflow, and by a large variety of polymorphic peptides identified.
KUPKB / Kidney & Urinary Pathway Knowledge Base
Provides a repository of multiomics data on kidney disease. KUPKB contains 220 data sets (mRNA, miRNA, proteins, phosphoprotein and metabolite expressions) extracted from specific kidney and urinary pathways (KUP) or generalistic databases and publications. Users can submit data via a spreadsheet template limited to specific terms of kidney and urinary pathways ontology (KUPO). The data can be visualized with the iKUP browser and it can return a molecule or list of molecules of interest.
mtsRPFdb / Mouse Tissue-Specific Ribosome Protected Fragment Database
Provides data of tissue-specific ribosome protected fragments in mice. mtsRPFdb offers about 28,500 genes’ transcriptional and translational expression information. It offers a web browser that permits users to filter the table by key words such as gene symbol gene ID or chromosome. This database can be useful for biological research community. It contains translational profiles of all the protein-coding genes for some mouse tissues (brain, heart, kidney, liver, lung, retina, spleen and testis).
tsORFdb
Obsolete
Lists all possible sORFs (Small Open Reading Frames) from whole genome sequence data that can be predicted through bioinformatic approaches. tsORFdb is a web-enabled database that was developed for all potential theoretical small ORFs (tsORFs) from the genome map. The tsORF information includes identification numbers of the tsORF, origin chromosome, origin frame, genomic start position, genomic end position, peptide sequence of the tsORF, and DNA sequence of the tsORF.
PDDB / Prion Disease Database
Obsolete
A comprehensive data resource on mouse prion diseases. PDDB contains: (i) time-course mRNA measurements spanning the interval from prion inoculation through appearance of clinical signs in eight mouse strain-prion strain combinations and (ii) histoblots showing temporal PrPSc accumulation patterns in brains from each mouse–prion combination. The database provides a suite of analytical tools for reconstructing dynamic networks via integration of temporal mRNA and interaction data and for analyzing these networks to generate hypotheses.

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