Blog Archives

Epitomy: Epitomy is a database which integrates scores of epitranscriptome sequencing datasets for exploring over a dozen types of post-transcriptional modifications on RNA transcripts in the human and mouse genomes

Epitomy is a database to integrate epitranscriptome sequencing data for exploring post-transcriptionally modifications of RNAs. Epitomy provides various search options such as searching by modification name, Pubmed ID, coordinates and gene name and is powered by IGV JS genome browser,

Lantern: A genome-scale lncRNA ontology annotation extractor and cellular network repository

Lantern is a repository of high quality controlled lncRNA ontology annotations, extracted by mining recent lncRNA literature using a robust NLP based approach. It also houses extensive lncRNA omics annotations like: tissue specific lncRNA expression, RBP interactions, lncRNA-protein co-expression, coding potential, sub-cellular localization and SNPs in

SliceIt: SliceIt is a CRISPR/Cas9 guide RNA prediction search engine to facilitate editing the protein-RNA interaction sites in the human genome

SliceIt is a genome-wide database of predicted sgRNAs based on CRISPR/Cas9 system to enable the systematic design of both low (gene or binding site centric) and high-throughput (genome-wide) CRISPR screens to understand the impact of editing the RNA-Binding Proteins’ binding

Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple developmental stages in eye tissues in mouse

Express contains transcript level expression data obtained from 21 lens and 35 retina RNA-Seq mouse samples. We downloaded the raw datasets, aligned them to reference genome and quantified transcript level expression for known and novel transcripts. When then downloaded the

Eye Splicer: Explore alternative splicing events across different developmental stages in lens from mouse samples

Eye Splicer is a genome browser powered by Biodalliance JavaScript library that lets you explore alternative splicing events across different developmental stages in lens from mouse samples. Eye Splicer contains the most abundant alternative splicing events, skipped exons and retained introns,

ExSurv: A web resource for prognostic analyses of exons across human cancers using clinical transcriptomes

ExSurv is a web resource for studying the survival contributions of exons across human cancers using RNA-seq data. ExSurv is the first web server which provides exon level survival significance by using the RNA-seq expression datasets and the clinical metadata

Seten: Gene Set Enrichment on CLIP-seq RNA-binding Protein Binding Signals Datasets

Seten is a tool for systematic identification and comparison of processes, phenotypes and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles. Seten is a web-based as well as a command line tool which can identify and compare processes, phenotypes

Operon Prediction for Bacterial Genomes DB (OperomeDB)

In prokaryotic organisms, a substantial fraction of adjacent genes are related functionally and most of these are organized into operons. Operons are a group of co-directionally organized genes in prokaryotic genomes with the presence of a common promoter and terminator.

RNA-binding Protein Expression and Disease Dynamics Database (READDB)

RNA-binding Protein Expression and Disease Dynamics database is a non-redundant, curated database of human RNA-binding proteins (RBPs). We collected RBPs data from multiple experimental studies and reported their annotation, tissue expression, microRNA predictions, disease associations, protein-protein interactions and their sequence