DATABASE and BIOINFORMATIC TOOLS

UCSC Genome Browser
An omics data consolidator, graphical viewer, and general bioinformatics resource
https://genome.ucsc.edu/

Ensembl
A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data
https://www.ensembl.org/index.html

R2 Genomics
A comprehensive, user-friendly platform for analyzing and interpreting genomic data, enabling them to make more informed decisions and advance their research in the field of genomics without the need for bioinformatics or coding expertise
https://hgserver1.amc.nl/cgi-bin/r2/main.cgi?open_page=login

GeneCards®: The Human Gene Database
GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. The knowledgebase automatically integrates gene-centric data from ~150 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.
https://www.genecards.org/

GeneSplicer
GeneSplicer is a flexible system for detecting splice sites in the genomic DNA of various eukaryotes.
http://www.cbcb.umd.edu/software/GeneSplicer/gene_spl.shtml

Gene Ontology Annotation (GOA) Database
The GO annotation program aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal.
https://www.ebi.ac.uk/QuickGO/

gnomAD
The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.
https://gnomad.broadinstitute.org/

RNAcentral
A comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms
https://rnacentral.org/

miRBase
A searchable database of published miRNA sequences and annotation
https://www.mirbase.org/index.shtml

miRTarbase
The experimentally validated microRNA-target interactions database
https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/index.php

miRDB
An online database for miRNA target prediction and functional annotations.
https://mirdb.org/

TargetScan
Search for predicted microRNA targets in mammals
https://www.targetscan.org/vert_80/

TarPmiR
Identification of microRNA target sites
http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/

StarMiR
Identification of microRNA target sites
https://sfold.wadsworth.org/cgi-bin/starmirWeb.pl

miRanda
An algorithm for finding genomic targets for microRNAs
https://cbio.mskcc.org/miRNA2003/miranda.html

LncExpDB
Expression Database of Human Long non-coding RNAs
https://ngdc.cncb.ac.cn/lncexpdb/

CircBase
Explore public circRNA datasets
http://www.circbase.org/

CircBank
A comprehensive database of human circRNA which included more than 140,000 human annotated circRNA from different source
http://www.circbank.cn/

ENCORI (Encyclopedia of RNA Interactomes)
An openly licensed and state-of-the-art platform to facilitate the integrative, interactive and versatile display of, as well as the comprehensive annotation and discovery of, RNA-RNA and protein-RNA interactions
https://rna.sysu.edu.cn/encori/

CircInteractome
A computationally identifies potential binding sites for RNA binding proteins within circRNAs
https://circinteractome.nia.nih.gov/

CSCD (Cancer-specific circRNAs database)
A database developed for cancer-specific circRNAs
http://gb.whu.edu.cn/CSCD/

deepBase
The most comprehensive expression analysis of sRNAs and lncRNAs, the expression patterns of tRFs and snoRNAs from thousands of cancer and normal samples, the correlations between ncRNAs and patients’ survival and the function prediction of ncRNAs in tumor tumorigenesis
https://rna.sysu.edu.cn/deepbase3/index.html

DIANA-mirPath
A miRNA pathway analysis web-server, providing accurate statistics, while being able to accommodate advanced pipelines. mirPath can utilize predicted miRNA targets (in CDS or 3’-UTR regions) provided by the DIANA-microT-CDS algorithm or even experimentally validated miRNA interactions derived from DIANA-TarBase. These interactions (predicted and/or validated) can be subsequently combined with sophisticated merging and meta-analysis algorithms
https://dianalab.e-ce.uth.gr/html/mirpathv3/index.php?r=mirpath

miRNet
A miRNA-centric network visual analytics platform
https://www.mirnet.ca/

DAVID (The Database for Annotation, Visualization and Integrated Discovery)
Provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes
https://david.ncifcrf.gov/

Protein Atlas
The open access resource for human proteins
https://www.proteinatlas.org/

PANTHER
To support biomedical and other research by providing comprehensive information about the evolution of protein-coding gene families, particularly protein phylogeny, function and genetic variation impacting that function
http://www.pantherdb.org/

ATtRACT
A daTabase of RNA binding proteins and AssoCiated moTifs
https://attract.cnic.es/

RBPmap
A computational tool that enables accurate prediction and mapping of RNA binding proteins (RBPs) binding sites on any RNA sequence or list of sequences of interest, provided by the users
http://rbpmap.technion.ac.il/index.html

UNIPROT
UniProt is the world’s leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information.
https://www.uniprot.org/

BLAST (Basic Local Alignment Search Tool)
BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance
https://blast.ncbi.nlm.nih.gov/Blast.cgi

Primer-BLAST
Finding primers specific to your PCR template
https://www.ncbi.nlm.nih.gov/tools/primer-blast/

Gene
Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
https://www.ncbi.nlm.nih.gov/gene/

GEO (Gene Expression Omnibus) DataSets
This database stores curated gene expression DataSets, as well as original Series and Platform records in the Gene Expression Omnibus (GEO) repository
https://www.ncbi.nlm.nih.gov/gds

MetaboAnalyst
A comprehensive platform dedicated for metabolomics data analysis via user-friendly, web-based interface
https://www.metaboanalyst.ca/

Aging Atlas
Aims to compile large gene expression and regulation datasets created by a range of high-throughput omics technologies and serve as a valuable resource for a range of life science researchers
https://ngdc.cncb.ac.cn/aging/index

Ovarian Kaleidoscope Database
Provides information regarding the biological function, expression pattern and regulation of genes expressed in the ovary
https://appliedbioinfo.com/

bioDBnet (biological DataBase network)
Allows for conversions of identifiers from one database to other database identifiers or annotations
https://biodbnet-abcc.ncifcrf.gov/db/db2db.php

VECTOR
uVeal mElanoma Correlation NeTwORk
https://vectordb.it/

COSMIC
the Catalogue of Somatic Mutations In Cancer
https://cancer.sanger.ac.uk/cosmic

Cellosaurus
A knowledge resource on cell lines
https://web.expasy.org/cellosaurus