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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

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Publication for SpliceDB

SpliceDB citations

 (3)
library_books

Conservation/Mutation in the Splice Sites of Cytokine Receptor Genes of Mouse and Human

2013
PMCID: 3877593
PMID: 24455408
DOI: 10.1155/2013/818954

[…] sites have been made in model species of vertebrates, invertebrates, fungi, protozoa, and plants [–]. comprehensive databases have also been generated, for example, http://www.softberry.com/spldb/splicedb.html [–], and []. cumulatively, the above-quoted papers report data on the global nucleotide patterns at the splice sites in each species, that is, the frequency of each base at a given […]

library_books

Inherited cobalamin malabsorption. Mutations in three genes reveal functional and ethnic patterns

2012
Orphanet J Rare Dis
PMCID: 3462684
PMID: 22929189
DOI: 10.1186/1750-1172-7-56

[…] and abcc1 were screened by dna sequencing in a selected group of patients (additional file )., suspected splice site changes were studied by comparing them to consensus sequences in splicedb []. if rna was available, first-strand cdna was produced from 0.5-1 μg total rna using the amv cdna synthesis kit (roche applied science, indianapolis, in) according to the instructions […]

library_books

A method of precise mRNA/DNA homology based gene structure prediction

2005
BMC Bioinformatics
PMCID: 1274302
PMID: 16242044
DOI: 10.1186/1471-2105-6-261

[…] are in the biggest group of gc-ag non-canonical splices sites, and the remaining 0.76% consist of small groups of size no more than 0.05% each. following the description in [] we parsed the human splicedb database of est supported, corrected and genbank high throughput genome sequencing projects (htg) supported pairs of non-canonical splice sites. then we aligned the pairs to the human refseq […]


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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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