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A compilation and categorization of alternative splicing resources : Probe set details
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
GatExplorer - Genomic and Transcriptomic Explorer
GATExplorer is an integrated database that combines genomic/transcriptomic visualization with nucleotide-level probe mapping.
Risueño A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics. 2010 Apr 29;11:221. PubMed PMID: 20429936; PubMed Central PMCID: PMC2875241.

Gene information includes chromosome location and gene description.
1)Displays gene splice variants and probe target locations for expression microarray platforms.  2)Provides a summary of splice variant coverage of multiple genes for common microarray platforms.  3)Provides high-througput analysis of peptide sequences indicating the splice variants that do / do not include the peptide. 
Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN. SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptIDe-based studies. BMC Bioinformatics. 2008 Jul 18;9:313. PubMed PMID: 18638396; PubMed Central PMCID: PMC2491637.

1) Gene information includes the chromosome number, strand, start, stop. 2) Peptide check displays the coding sequence for a peptide within splice variant of a gene. 3) Expression- check provides visualization of microarray expression data for a gene 4) Batch tools are also provided.
SpliceMiner is a tool for querying Evidence Viewer Database (EVDB). SpliceMiner supports high-throughput batch queries and provides results in an easily parsable format.
Kahn AB, Ryan MC, Liu H, Zeeberg BR, Jamison DC, Weinstein JN. SpliceMiner: a high-throughput database implementation of the NCBI EvIDence Viewer for microarray splice variant analysis. BMC Bioinformatics. 2007 Mar 5;8:75. PubMed PMID: 17338820; PubMed Central PMCID: PMC1839109.

1) Gene information includes chromosome number, start and end position, strand information. 2) Probe information includes Probe position.
Yates T, Okoniewski MJ, Miller CJ. X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis. Nucleic AcIDs Res. 2008 Jan;36(Database issue):D780-6. Epub 2007 Oct 11. PubMed PMID: 17932061; PubMed Central PMCID: PMC2238884.
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