AltAnalyze is a comprehensive tool for the analysis of gene expression and alternative splicing data from RNA-seq and Affymetrix (exon, gene, junction) datasets at the level of proteins, domains, microRNA binding sites and pathways. The Cytoscape plugin DomainGraph (www.domaingraph.de) allows for visualization of AltAnalyze results at multiple levels of abstraction (e.g., isoform, exon, protein, domain, molecular interactions).
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.
ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.
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.
Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.
AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.
AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.
A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice.
Database which stores alternative splicing information generated from EST, mRNA and protein alignments with genomic sequence; text-based queries and graphical views of putative splice variants.
Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.
Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites.