Plann: A Command-Line Application for Annotating Plastome Sequences

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...

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Bibliographic Details
Published inApplications in plant sciences Vol. 3; no. 8
Main Authors Huang, Daisie I, Cronk, Quentin C. B
Format Journal Article
LanguageEnglish
Published United States Botanical Society of America 01.08.2015
John Wiley & Sons, Inc
Subjects
Annotations
Automation
Biotechnology
chloroplast
computer software
GenBank
Genes
genetic databases
genome annotation
Genomes
Internet
Mutation
National Center for Biotechnology Information
Phylogenetics
Phylogeography
pipelines
Plant sciences
plastome
Sequin
SOFTWARE NOTE
chloroplast
plastome
genome annotation
GenBank
Sequin
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Summary: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.
Bibliography:This contribution was written while D.I.H. was salaried via the Genome Canada Large‐Scale Applied Research Project (grant no. 168BIO: PIs Carl Douglas and Shawn Mansfield, University of British Columbia). Q.C.B.C. acknowledges support from the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grants Program (grant no. RGPIN‐2014‐05820).
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This contribution was written while D.I.H. was salaried via the Genome Canada Large-Scale Applied Research Project (grant no. 168BIO: PIs Carl Douglas and Shawn Mansfield, University of British Columbia). Q.C.B.C. acknowledges support from the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grants Program (grant no. RGPIN-2014-05820).
ISSN:2168-0450
2168-0450
DOI:10.3732/apps.1500026