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Publication for SpliceDB
The paralog to contig assignment problem: high quality gene models from fragmented assemblies
[…] d by automatic means.At present, there are no databases that simultaneously provide both, paralogy information and accurate information on exon-intron structure. The Exon-Intron database (EID)  and SpliceDB  do not provide information on paralogs; Ensembl Compara on the other hand, does not provide homology information for individual exons. The lack of a gold standard makes it unfeasible to qu […]
Linking the Epigenome to the Genome: Correlation of Different Features to DNA Methylation of CpG Islands
[…] the whole human genome is used as a feature. We used ModuleMaster to apply the PFMs to the sequences and calculate the weight scores.Splice sites (5 features). We used all four PFMs, generated from SpliceDB to identify splice sites. The four PFMs correspond to mammalian frequency matrices of splice sites for GT-AG and GC-AG pairs for donor and acceptor sites respectively. These four features we […]
BIPASS: BioInformatics Pipeline Alternative Splicing Services
[…] e 64 bit processors operating on RedHat Enterprise Linux 4, 64 bit version. Wrappers were developed to access and retrieve data from multiple public resources, e.g. GenBank (Entrez Nucleotide). BIPAS-SpliceDB exploits data stored a priori in the WSII data warehouse, whereas BIPAS-Align-&-Splice processes the users’ input and stores the data in the WSII database where the pipeline (alignment and sp […]
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