dRNA mapper specifications

Information


Unique identifier OMICS_16363
Name dRNA mapper
Interface Web user interface
Restrictions to use None
Input data A sequence of the gene of interest, a selection of dRNAdb.
Input format FASTA
Output data The matching dRNA reads, a dRNA read map of the input transcript.
Programming languages Javascript, Perl
Computer skills Basic
Stability No
Maintained No

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Maintainer


This tool is not available anymore.

Publication for dRNA mapper

dRNA mapper in publications

 (2)
PMCID: 5286533
PMID: 28145468
DOI: 10.1038/srep41052

[…] 5′5.8s rrfs from other plant species from the psrnatarget. to further validate the predicted cleavage on the srna–target pairs, the degradome library was searched for the cleavage product using the drna mapper tool from somart web server (http://somart.ist.berkeley.edu). the cleavage from the predicted target of a. thaliana was analysed from the pare (parallel analysis of rna ends) sequencing […]

PMCID: 4161772
PMID: 25178990
DOI: 10.1186/1471-2164-15-743

[…] of tomato i2 homologues were also investigated using a degradome database using online program somart []. first, a randomly chosen tomato i2 homologue was input into programs silcer detector and drna mapper. the output of these two programs was then analyzed by a third program smart compar., using blastn method, 36 i2 homologues were discovered in the sequenced genome of tomato cultivar […]


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dRNA mapper institution(s)
Department of Plant and Microbial Biology, Plant Gene Expression Center, University of California, Berkeley, CA, USA; United States Department of Agriculture-Agricultural Research Services, Albany, CA, USA
dRNA mapper funding source(s)
This work was supported by the National Science Foundation Plant Genome Research Program Grant (DBI-0218166) and the United States Department of Agriculture (CRIS 5335-22000-007-00D).

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