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SpliceDB specifications

Information


Unique identifier OMICS_04045
Name SpliceDB
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for SpliceDB

SpliceDB citations

 (3)
library_books

The paralog to contig assignment problem: high quality gene models from fragmented assemblies

2016
PMCID: 4765045
PMID: 26913054
DOI: 10.1186/s13015-016-0063-y

[…] 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 […]

library_books

Linking the Epigenome to the Genome: Correlation of Different Features to DNA Methylation of CpG Islands

2012
PLoS One
PMCID: 3340366
PMID: 22558141
DOI: 10.1371/journal.pone.0035327

[…] 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 […]

library_books

BIPASS: BioInformatics Pipeline Alternative Splicing Services

2007
Nucleic Acids Res
PMCID: 1933140
PMID: 17584795
DOI: 10.1093/nar/gkm344

[…] 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 […]

Citations

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SpliceDB institution(s)
Department of Electrical and Computing Engineering, Department of Bioinformatics and Systems Biology, and Department of Computer Science, University of California, San Diego, La Jolla, CA, USA

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