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. 2015 Aug 10;3(8):apps.1500026.
doi: 10.3732/apps.1500026. eCollection 2015 Aug.

Plann: A command-line application for annotating plastome sequences

Daisie I Huang  1 , Quentin C B Cronk  1
Affiliations

Plann: A command-line application for annotating plastome sequences

Daisie I Huang et al. Appl Plant Sci. .

Abstract

Premise of the study: Plann automates the process of annotating a plastome sequence in GenBank format for either downstream processing or for GenBank submission by annotating a new plastome based on a similar, well-annotated plastome.

Methods and results: Plann is a Perl script to be executed on the command line. Plann compares a new plastome sequence to the features annotated in a reference plastome and then shifts the intervals of any matching features to the locations in the new plastome. Plann's output can be used in the National Center for Biotechnology Information's tbl2asn to create a Sequin file for GenBank submission.

Conclusions: Unlike Web-based annotation packages, Plann is a locally executable script that will accurately annotate a plastome sequence to a locally specified reference plastome. Because it executes from the command line, it is ready to use in other software pipelines and can be easily rerun as a draft plastome is improved.

Keywords: GenBank; Sequin; chloroplast; genome annotation; plastome.

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Figures

Fig. 1.
Fig. 1.
For each GenBank record along the x-axis, the number of genes annotated by Plann for the raw plastome sequence is represented by a bar. Note that the self-to-self annotation is always equivalent to the number of genes present in the original GenBank record.
See this image and copyright information in PMC

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