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mirMachine: A One-Stop Shop for Plant miRNA Annotation

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Plann: A command-line application for annotating plastome sequences.

Daisie I Huang¹, Quentin C B Cronk¹

¹Department of Botany, University of British Columbia, 3529-6270 University Blvd.,Vancouver, British Columbia V6T 1Z4, Canada.

Applications in Plant Sciences

|August 28, 2015

Summary

Plann is a command-line script that automates plastome sequence annotation by using a reference genome. This tool facilitates efficient GenBank submission and integration into bioinformatics pipelines.

Keywords:

GenBank Sequin chloroplast genome annotation plastome

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Area of Science:

Genomics
Bioinformatics

Background:

Plastome annotation is crucial for understanding organelle genomes.
Manual annotation is time-consuming and prone to errors.

Purpose of the Study:

To develop an automated tool for plastome annotation.
To streamline the process for GenBank submission and downstream analysis.

Main Methods:

Plann is a Perl script executed via the command line.
It compares a target plastome sequence to a reference plastome.
Feature intervals are shifted to match the new sequence locations.

Main Results:

Plann generates annotated plastome data compatible with NCBI's tbl2asn.
The script enables the creation of Sequin files for GenBank submission.
Output is suitable for further processing in bioinformatics workflows.

Conclusions:

Plann offers a locally executable alternative to web-based annotation tools.
It provides accurate annotation based on user-defined reference plastomes.
The script's command-line nature allows seamless integration into automated pipelines and iterative refinement.