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Bioinformatics. 2016 Feb 1;32(3):450-2. doi: 10.1093/bioinformatics/btv583. Epub 2015 Oct 10.

miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis.

Author information

1
Center for Bioinformatics and Computational Biology and Delaware Biotechnology Institute and.
2
Delaware Biotechnology Institute and.
3
Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA.
4
Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA.

Abstract

SUMMARY:

We describe miTRATA, the first web-based tool for microRNA Truncation and Tailing Analysis--the analysis of 3' modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. miTRATA is implemented in Python (version 3) and employs parallel processing modules to enhance its scalability when analyzing multiple small RNA (sRNA) sequencing datasets. It utilizes miRBase, currently version 21, as a source of known microRNAs for analysis. miTRATA notifies user(s) via email to download as well as visualize the results online. miTRATA's strengths lie in (i) its biologist-focused web interface, (ii) improved scalability via parallel processing and (iii) its uniqueness as a webtool to perform microRNA truncation and tailing analysis.

AVAILABILITY AND IMPLEMENTATION:

miTRATA is developed in Python and PHP. It is available as a web-based application from https://wasabi.dbi.udel.edu/∼apps/ta/.

CONTACT:

meyers@dbi.udel.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26454275
DOI:
10.1093/bioinformatics/btv583
[Indexed for MEDLINE]

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