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

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.

SUBMITTER: Huang DI

PROVIDER: S-EPMC4542940 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature

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

Huang Daisie I DI Cronk Quentin C B QC

Applications in plant sciences 20150810 8

<h4>Premise of the study</h4>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.<h4>Methods and results</h4>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 ...[more]

PMID: 26312193

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