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Database Guide

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The Allen Brain Atlas (ABA) is an interactive, genome-wide image database of gene expression in the mouse brain. A combination of RNA in situ hybridization data, detailed Reference Atlases and informatics analysis tools are integrated to provide a searchable digital atlas of gene expression. Together, ... [Information of the supplier]
In bacteria, small (~30-500 nt) non-coding RNAs (sRNAs) are the most abundant class of post-transcriptional regulators that are involved in diverse processes including quorum sensing, stress response, virulence and carbon metabolism. Based on the target molecules, sRNAs can be divided into two major ... [Information of the supplier]
ChIPBase, an integrated resource and platform for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs(snoRNAs, tRNAs, snRNAs, etc.) and protein-coding genes from ChIP-Seq data. ChIPBase ... [Information of the supplier]
The Database for Aligned Ribosomal Complexes (DARC) site provides a resource for directly comparing the structures of available ribosomal complexes. The site offers a collection of files deposited in the RCSB protein data bank and the Electron Microscopy Data Bank, which have been aligned so as to make ... [Information of the supplier]
Viral siRNA Database (VIRsiRNAdb) is a structured collection of experimentally validated siRNAs reported in the scientific literature targeting diverse genes of important human viruses. The curation efforts to date has concentrated mainly on viruses known to be associated with infectious diseases in ... [Information of the supplier]
LncBase hosts elaborated information for, both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA ... [Information of the supplier]
In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatori... [Miscellaneous as indicated]
The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools presented by greengenes can assist the researcher in choosing phylogenetically specific probes, interpreting microarray ... [Information of the supplier]
JASPAR is a collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. JASPAR is the only database with this scope where the data can be used with no restrictions (open-source)... [Information of the supplier]
The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with ... [Information of the supplier]
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