Open AccessPlann: A command‐line application for annotating plastome sequences
Author(s) -
Huang Daisie I.,
Cronk Quentin C. B.
Publication year - 2015
Publication title -
applications in plant sciences
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.64
H-Index - 23
ISSN - 2168-0450
DOI - 10.3732/apps.1500026
Subject(s) - chloroplast dna , genbank , perl , annotation , computer science , line (geometry) , biology , artificial intelligence , genetics , programming language , genome , mathematics , gene , geometry
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.