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ASPicDB specifications

Information


Unique identifier OMICS_01882
Name ASPicDB
Restrictions to use None
Maintained No
Wikipedia https://en.wikipedia.org/wiki/AspicDB

Taxon


  • Primates
    • Homo sapiens

Publication for ASPicDB

ASPicDB citations

 (7)
library_books

A survey of software for genome wide discovery of differential splicing in RNA Seq data

2014
Hum Genomics
PMCID: 3903050
PMID: 24447644
DOI: 10.1186/1479-7364-8-3

[…] oals downstream of alternative splicing analysis are to identify the regulatory differences in the transcript isoforms and the functional differences in the encoded protein isoforms. In this respect, ASPicDB (http://www.caspur.it/ASPicDB/) is a database of human protein variants generated by AS []. AltAnalyze has begun to address the consequences of AS by incorporating protein domain annotations i […]

library_books

Alternative Splicing for Diseases, Cancers, Drugs, and Databases

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

[…] uences which modulate the 3′ end processing of pre-mRNAs.Additionally, several comprehensive databases for alternative splicing have been developed such as HOLLYWOOD [], ASD [], BIPASS [], ECgene [], ASPicDB [], AspAlt [], H-DBAS [], SPLOOCE [], and APPRIS []. For example, the ECgene provides EST and serial analysis of gene expression (SAGE) data-based annotation and visualization for alternative […]

library_books

A Novel Computational Strategy to Identify A to I RNA Editing Sites by RNA Seq Data: De Novo Detection in Human Spinal Cord Tissue

2012
PLoS One
PMCID: 3434223
PMID: 22957051
DOI: 10.1371/journal.pone.0044184

[…] g as main parameters: -B 5 -t 10 -d ann –pairmax-dna = 500 -n 3000–fails-as-input -a paired -O) onto the assembled transcriptome including more than 370,000 transcripts from Ensembl, UCSC, RefSeq and ASPiCdb. Custom python scripts were then used to parse GSNAP results, filtering out inconsistent alignments due to reads with more than two Ns characters and very low quality scores. The same scripts […]

library_books

BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments

2012
BMC Bioinformatics
PMCID: 3314565
PMID: 22536968
DOI: 10.1186/1471-2105-13-S4-S21

[…] pathways involved; Gene Ontology (GO) database [], that provides a controlled vocabulary of terms which describe gene product characteristics and gene product annotation data.- Specialized database: ASPicDB [], a database designed to provide information and reliable annotations of the AS pattern of human genes; FeatDB, a custom database reporting chromosomal location about known (RefSeq) human tr […]

library_books

PEPPI: a peptidomic database of human protein isoforms for proteomics experiments

2010
BMC Bioinformatics
PMCID: 3026381
PMID: 20946618
DOI: 10.1186/1471-2105-11-S6-S7

[…] ed for comprehensive protein isoform identification purposes.Although there are several publicly available alternative splicing mRNA transcript databases and SNP databases including ASTD [], EID [,], ASPicDB [], ECgene [], MutDB [,], and dbSNP [], none of these databases can be readily used for identification of novel peptides derived from uncharacterized protein isoforms. Since predictions of gen […]

library_books

Assessment of orthologous splicing isoforms in human and mouse orthologous genes

2010
BMC Genomics
PMCID: 3091683
PMID: 20920313
DOI: 10.1186/1471-2164-11-534

[…] eading frame, we used only one representative in our analyses.As well as comparing human and mouse RefSeq collections, we also compared the RefSeq transcript collection to the transcripts included in ASPicDB [], which collects all putative alternative isoforms for a given gene determined by the ASPIC algorithm [,]. ASPIC first performs a multiple alignment of all full-length transcripts and ESTs o […]

Citations

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ASPicDB institution(s)
Biocomputing Group, University of Bologna, Bologna, Italy

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