Plann: A command-line application for annotating plastome sequences

By Daisie I. Huang, Q. Cronk. Applications in Plant Sciences, 2015

394 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/428a1b0c219c77cb18679e2a0110490f5890fb1f

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In Molecular Biology

1. Chang Liu
2. Peter Poczai
3. Haimei Chen
4. Ali Amiryousefi
5. Linchun Shi
6. Jing Tang
7. Jaakko Hyvönen
8. Shuyu Zheng

Citations in the corpus

• Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes (2020, methodology): “…solely optimized for assembling (GetOrganelle: Jin et al., 2019; FastPlast: McKain and Wilson, 2017; MITObim: Hahn et al., 2013), annotating (Plann: Huang and Crong, 2015; MITOS: Bernt et al., 2013), and analyzing organelle genomes (Chlorobox: Tillich et al., 2017; CPGAVAS2: Shi et al., 2019).”
• CPGView: A package for visualizing detailed chloroplast genome structures (2023, methodology): “…visualization tools have been developed for organelle genomes; these tools include DOGMA (Wyman et al., 2004), CPGAVAS (Liu et al., 2012), Plann (Huang & Cronk, 2015), Verdant (McKain et al., 2017), GeSeq (Tillich et al., 2017 ), AGORA (Jung et al., 2018), OrganellarGenomeDRAW version 1.3.1…”
• CPGAVAS2, an integrated plastome sequence annotator and analyzer (2019, methodology): “Plann and AGORA support user-provided dataset as reference.”