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RNA MISCELLANEA


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Gene Quantification: qPCR protocols logo

The Gene Quantification page describes and summarises all technical aspects involved in quantitative gene expression analysis using real-time qPCR & qRT-PCR.

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Alternative Splicing Database Project logo
Category: RNA miscellanea
Subcategories: EMBL

The Alternate Transcript Diversity Project (ATD) Project aims to understand the mechanisms that are responsible for the formation of transcript isoforms on a genome-wide scale by creating a value-added database of full-length alternate transcripts from human and mouse.

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Rfam logo
Category: RNA miscellanea

Rfam is a collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. The main use of Rfam is as a source of RNA multiple alignments with consensus secondary structure annotation in a consistent format. In conjunction with the Infernal software package, Rfam covariance models (CMs) can be used to search genomes or other DNA sequence databases for homologs to known structural RNA families.

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AREsite logo
Category: RNA miscellanea

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 30-untranslated regions (UTRs. In its current version AREsite uses Ensembl release 56 as data basis (Gruber et al., Nucleic Acid Res 39:D66, 2011).

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SILVA logo
Category: RNA miscellanea

SILVA is a comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data, free for academic use. SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

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NONCODE logo
Category: RNA miscellanea

NONCODE is a database of all kinds of noncoding RNAs (except tRNAs and rRNAs).

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ASPicDB (Alternative splicing) logo
Category: RNA miscellanea

ASPicDB is a database designed to provide access to reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm, and to the functional annotation of predicted isoforms (Martelli et al., Nucleic Acids Res 39:D80, 2011)

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RNAGASP consortium logo
RNA-seq Genome Annotation Assessment Project
Category: RNA miscellanea

The RNA-seq Genome Annotation Assessment Project (RGASP) is designed to evaluate computational methods for RNA-seq data analysis. The primary goals of RGASP are to assess RNA-seq alignment, transcript reconstruction and quantification software, and to determine the feasibility of automated genome annotation based on transcriptome sequencing. RGASP is organized in a consortium framework

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