Splicing

There are links that deal with the splicing of gene sequences in this section.

Found 26 links

Displaying 15 links

AltAnalyzeTool Content

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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).

This content is being maintained by NathanSalomonis.

Alternative Splicing Database (ASD) ProjectDatabase Content

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Access to the AltSplice, AltExtron and AEdb databases.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

Alternative Splicing GalleryDatabase Content

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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.

ASPicTool Content

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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.

AStalavistaTool Content

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AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.

AUGUSTUSTool Content

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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.

This content is being maintained by Mario Stanke.

Database for Bacterial Group 2 IntronsDatabase Content

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Database for Bacterial Group 2 Introns: a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. General info on group 2 intron properties, structures and classification. Lists info for individual introns (insertion sites, DNA sequences, intron-encoded protein sequences, RNA secondary structure models). Tools fo ridentification and analysis of intron sequences.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
Database for bacterial group II introns20121

Exon Array AnalyzerTool Content

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The Exon Array Analyzer (EAA) allow to process CEL files from Affymetrix, Inc. GeneChip® Exon 1.0 ST Arrays. Various processign steps and visualizations are implemented to identify alternative splicing events. Three simple steps have to be performed to submit a set of CEL files. After the processing is completed the results can be viewed in the browser.

Gene Array AnalyzerTool Content

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The Gene Array Analyzer (GAA) allow to process CEL files from GeneChip® Gene 1.0 ST Arrays. Various processing steps and visualizations are implemented to identify alternative splicing events. Three simple steps have to be performed to submit a set of CEL files. After the processing is completed the results can be viewed in the browser.

GeneSplicerTool Content

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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.

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