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Protocols

ASTD specifications

Information


Unique identifier OMICS_09529
Name ASTD
Alternative name Alternative Splicing and Transcript Diversity
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Maintained No
Wikipedia https://en.wikipedia.org/wiki/Alternative_splicing_and_transcript_diversity_database

Maintainer


This tool is not maintained anymore.

Publications for Alternative Splicing and Transcript Diversity

ASTD citations

 (15)
call_split

A Reverse Genetics Mutational Analysis of the Barley HvDWARF Gene Results in Identification of a Series of Alleles and Mutants with Short Stature of Various Degree and Disturbance in BR Biosynthesis Allowing a New Insight into the Process

2016
Int J Mol Sci
PMCID: 4849053
PMID: 27110778
DOI: 10.3390/ijms17040600
call_split See protocol

[…] software [] (National Center for Biotechnology Information: Bethesda, MD, USA). The ASD—Alternative Splicing tool (The European Bioinformatics Institute: Cambridge, UK) [,], which is now part of the ASTD—Alternative Splicing and Transcript Diversity Databases, was applied to determine the position of mutation (allele brd1-d) with respect to the donor site, branch point, polypyrimidine tract and a […]

library_books

Alternative Splicing for Diseases, Cancers, Drugs, and Databases

2013
Sci World J
PMCID: 3674688
PMID: 23766705
DOI: 10.1155/2013/703568

[…] Both PolyA_DB [] and AltTrans provide the information for alternative polyadenylation []. For AltTrans, the AltSplice pipeline on splicing and the AltPAS pipeline on polyadenylation were implemented. ASTD [] also provides the variants for splicing, transcription initiation, and polyadenylation. Of note, the dataset of transcriptomics for alternative splicing is larger than for alternative polyaden […]

library_books

The Cancer Exome Generated by Alternative mRNA Splicing Dilutes Predicted HLA Class I Epitope Density

2012
PLoS One
PMCID: 3458037
PMID: 23049726
DOI: 10.1371/journal.pone.0038670

[…] I supertype representatives are more common than others. It is therefore expected that for the less frequent HLA alleles, the results are more likely to include noise. The source of our data set, the ASTD database, is to a large extent originating from EST data without HLA specific information. EST data is mostly based on Caucasian Europeans ; therefore we can safely assume that the more common HL […]

library_books

A Novel MCPH1 Isoform Complements the Defective Chromosome Condensation of Human MCPH1 Deficient Cells

2012
PLoS One
PMCID: 3431399
PMID: 22952573
DOI: 10.1371/journal.pone.0040387

[…] We first screened the databases for the existence of alternatively spliced MCPH1 transcripts. In addition to full-length MCPH1 (MCPH1-FL), the Alternative Splicing and Transcript Diversity database (ASTD) includes a variant lacking the first three exons (MCPH1Δe1–3) and another lacking exons 9–14 (MCPH1Δe9–14) (). The latter is also registe […]

library_books

A graph based approach for designing extensible pipelines

2012
BMC Bioinformatics
PMCID: 3496580
PMID: 22788675
DOI: 10.1186/1471-2105-13-163

[…] o convert αinto β, we would have Wαβ(Tαβ); to convert α into γ, we would have Wαγ(TαβTβγ); and to convert α into δ, we would have Wαδ(TαβTβδ). If a new conversion tool is added into this system, such asTδ∈, additional workflows are needed to implement the new functionality (in this case, Wδ∈, Wα∈ and Wβ∈). Without an automated process for composing workflows, these new workflows have to be created […]

library_books

Skipping of Exons by Premature Termination of Transcription and Alternative Splicing within Intron 5 of the Sheep SCF Gene: A Novel Splice Variant

2012
PLoS One
PMCID: 3376141
PMID: 22719917
DOI: 10.1371/journal.pone.0038657

[…] CF polyadenylation sites were predicted using the polyADQ web server . Alternative splicing pattern of the ovine SCF transcripts with human, mouse reference assembly were predicted using ACEVIEW and Alternative Splicing and Transcript Diversity (ASTD 1.1) . The splice site prediction such as putative alternative exon isoform, cryptic and constitutive splice sites of internal (coding) exons was pe […]

Citations

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ASTD institution(s)
European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany; South African National Bioinformatics Institute, University Western Cape, Bellville, South Africa; Estonian Biocenter, Tartu, Estonia; University of Tartu, Tartu, Estonia; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Grup de Recerca en Informatica Biomedica, Institut Municipal d'Investigacio Medica, Universistat Pompeu Fabra, Barcelona, Spain; INSERM U928, Université de la Méditerranée, Marseille, France; Center for Bioinformatics, University of Hamburg, Hamburg, Germany; Institute for Clinical Molecular Biology, Christian-Albrechts University Kiel, University Hospital Schleswig-Holstein, Kiel, Germany; Department of Bioinformatics, Max-Delbrueck-Center for Molecular Medicine Berlin-Buch, Berlin, Germany; Center for Genomic Regulation, Barcelona, Spain
ASTD funding source(s)
Supported by the European Commission FP6 Programme, contract number LSHG-CT-2003-503329.

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