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DEDB specifications

Information


Unique identifier OMICS_01894
Name DEDB
Alternative name Drosophila melanogaster Exon Database
Restrictions to use None
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster

Publication for Drosophila melanogaster Exon Database

DEDB citations

 (4)
library_books

C. elegans SUP 46, an HNRNPM family RNA binding protein that prevents paternally mediated epigenetic sterility

2017
BMC Biol
PMCID: 5513350
PMID: 28716093
DOI: 10.1186/s12915-017-0398-y

[…] expressed. To examine alternative splicing, transcripts in the WS220 version of WormBase were classified into different types of alternative splicing events using two different methodologies, namely DEDB (http://proline.bic.nus.edu.sg/dedb/methodology.html) and SpliceTrap (http://rulai.cshl.edu/splicetrap/). Information on the classes of alternative splicing events and the classification process […]

call_split

Involvement of PARP1 in the regulation of alternative splicing

2016
PMCID: 4860959
PMID: 27462443
DOI: 10.1038/celldisc.2015.46
call_split See protocol

[…] cbcb.umd.edu/software/GeneSplicer); Splice Site Prediction by Neural Network (http://www.fruitfly.org/seq_tools/splice.html); NNSPLICE 0.9 version (http://www.fruitfly.org/seq_tools/splice.html); and Drosophila Melanogaster Exon Database (http://proline.bic.nus.edu.sg/dedb/cgi-bin/viewer.py?id=13068). I n silico PCR program, http://genome.ucsc.edu/index.html?org=Hu​man&db=hg18&hgsid=142437216 was […]

library_books

Molecular evolution of Drosophila Sex lethal and related sex determining genes

2012
BMC Evol Biol
PMCID: 3292462
PMID: 22244243
DOI: 10.1186/1471-2148-12-5

[…] the Mafft software (v6.624 beta) [] using the E-INS-i option with default parameters. Exon boundaries were checked for the Drosophila species using the Jalview visualization software (v11) [] and the DEDB database []. Before proceeding with selection analyses, all positions containing indels were removed from the alignment. Complete alignments are provided in the Additional Files accompanying this […]

library_books

Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse

2009
BMC Genomics
PMCID: 2709266
PMID: 19594882
DOI: 10.1186/1471-2164-10-S1-S5

[…] s as nodes, interconnected by introns as edges, with paths through the splicing graph representing the transcripts. Such a schema was applied to the Drosophila melanogaster genome [], to generate the DEDB data resource. Here, the first transcript served as a reference sequence to generate splicing graphs, with automatic rule-based classification of splicing events. The use of exons and introns as […]

Citations

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DEDB institution(s)
Department of Biochemistry, National University of Singapore, Singapore

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