title: Plann: A command-line application for annotating plastome sequences.
abstract: OBJECTIVE
  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.
  
  
  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.
authors: Department of Botany, University of British Columbia, 3529-6270 University Blvd.,Vancouver, British Columbia V6T 1Z4, Canada.
authors: Daisie I
authors: DI
authors: Huang
authors: Department of Botany, University of British Columbia, 3529-6270 University Blvd.,Vancouver, British Columbia V6T 1Z4, Canada.
authors: Quentin C B
authors: QC
authors: Cronk
keywords: GenBank; Sequin; chloroplast; genome annotation; plastome