The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one or more exons and download the resulting sequence. ASG also links out to other alternative splicing databases like ProSplicer.
AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREsite allows one to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. A detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1 is also provided.
Alignment of RNA Tertiary Structures (ARTS) is a method for aligning two nucleic acid structures (RNAs or DNAs) and detecting a-priori unknown common substructures.
AsiDesigner is a design software system for siRNA design, that takes into account alternative splicing for mRNA level gene silencing. The software also has the capacity to design siRNAs for silencing of multiple mRNAs simultaneously, to score the performance of designed siRNAs, to search for off-targets with BLAST and FASTA algorithms, and to check for secondary structure energy of siRNAs.
Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.
Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.
Recognizing the growing role for non-coding RNAs (ncRNAs) in cells, the CentroidFold web server predicts RNA secondary structure from input sequence data (single or multiple alignments).
CLIPZ supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other type of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The CLIPZ platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets.
CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment. The 3D sequence logo consists of a square matrix that shows columns with high mutual information, a measure of how much the residues in two alignment columns are correlated.
Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.
deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. deepBase facilitates the comprehensive annotation and discovery of small RNAs from transcriptomic data such as ncRNA-associated small RNAs (nasRNAs), promoter-associated small RNAs (pasRNAs), exon-associated small RNAs (easRNAs), repeat-associated small RNAs (rasRNAs) and miRNA and snoRNA candidates. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display.
The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.
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