sRNA mapper specifications


Unique identifier OMICS_16365
Name sRNA mapper
Interface Web user interface
Restrictions to use None
Input data The gene sequence, the selected sRNAdb.
Input format FASTA
Output data The sRNA reads mapped to the gene of interest, the phasing pattern of sRNAs mapped to the input sequence, the statistics for the length distribution and 5' end composition of sRNAs, the sRNA mapping profile.
Programming languages Javascript, Perl
Computer skills Basic
Stability No
Maintained No


  • Plants and Fungi
    • Arabidopsis thaliana


This tool is not available anymore.

Publication for sRNA mapper

sRNA mapper in publication

PMCID: 5209821
PMID: 28052756
DOI: 10.1186/s12864-016-3394-7

[…] reads were removed using the duster tool from the ngs toolbox. the resulting sequences were mapped to the bos taurus 3.1 (bt3.1) genome assembly and to chromosome y from the 4.6.1 assembly with srna mapper. only the best-scoring alignments were taken into account, and up to two non-templated 3′ nucleotides were allowed in order to successfully map sequences that were subject […]

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sRNA 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
sRNA mapper funding source(s)
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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