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Citations per year

Number of citations per year for the bioinformatics software tool ASIP
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chevron_left Alternative splicing detection Alternative splicing events identification chevron_right
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ASIP specifications

Information


Unique identifier OMICS_18340
Name ASIP
Alternative name Alternative Splicing in Plants
Interface Web user interface
Restrictions to use None
Input data Some genome sequences.
Input format FASTA
Output data List and annotation of alternatively spliced genes; Intron, exon, and junction sequences; Raw GeneSeqer alignment, MySQL database dump.
Output format TXT
Programming languages Perl
Computer skills Basic
Stability Stable

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Glycine max
    • Hordeum vulgare
    • Medicago truncatula
    • Oryza sativa
    • Populus trichocarpa
    • Triticum aestivum
    • Vitis vinifera

Versioning


No version available

Maintainers


This tool is not maintained anymore.

Publication for Alternative Splicing in Plants

ASIP citations

 (3)
library_books

Evolutionary Character of Alternative Splicing in Plants

2016
Bioinform Biol Insights
PMCID: 4721685
PMID: 26819552
DOI: 10.4137/BBI.S33716

[…] Although plenty of analyses of AS in plants have been presented and a huge quantity of data produced, it is necessary to think about the most efficient way to display these data. An AS database, eg, Alternative Splicing in Plants (ASIP), and genome browser tracks that are open source and easy to download may be the best choice.Also, since AS was affected by many factors, such as time, stress, and […]

library_books

Towards improved genome scale metabolic network reconstructions: unification, transcript specificity and beyond

2015
Brief Bioinform
PMCID: 5142010
PMID: 26615025
DOI: 10.1093/bib/bbv100

[…] from ENSEMBL [] and from the Integrated Pathway Analysis database are used to create artificial transcripts and peptides.While all databases mentioned above are focusing on different vertebrates, the ASIP database is specialized to plants []. It allows the visualization of alternative splice forms in plants like A. thaliana or Oryza sativa. To obtain the annotations, the ASIP database uses an auto […]

library_books

Analysis of pollen specific alternative splicing in Arabidopsis thaliana via semi quantitative PCR

2015
PeerJ
PMCID: 4419537
PMID: 25945312
DOI: 10.7717/peerj.919

[…] t in leaf versus pollen. We also observed a small number of unspliced reads that aligned to the differentially spliced intron, indicating a low level of intron retention (not shown), a common form of alternative splicing in plants ().To validate the RNA-Seq results, we designed PCR primers flanking the differentially spliced region and performed semi-quantitative PCR using newly prepared pollen an […]


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ASIP institution(s)
Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA; Department of Genetics, Development and Cell Biology and Department of Statistics, Iowa State University, Ames, IA, USA; Pioneer Hi-Bred International, Johnston, IA, USA
ASIP funding source(s)
Supported by National Science Foundation grants DBI-0321460 and DBI-0606966, NSF grant DBI-0606909.

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