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

Huang DI, Cronk QC - Appl Plant Sci (2015)

Bottom Line: Plann's output can be used in the National Center for Biotechnology Information's tbl2asn to create a Sequin file for GenBank submission.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, University of British Columbia, 3529-6270 University Blvd.,Vancouver, British Columbia V6T 1Z4, Canada.

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.

No MeSH data available.


For each GenBank record along the x-axis, the number of genes annotated by Plann for the raw plastome sequence is represented by a bar. Note that the self-to-self annotation is always equivalent to the number of genes present in the original GenBank record.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4542940&req=5

fig1: For each GenBank record along the x-axis, the number of genes annotated by Plann for the raw plastome sequence is represented by a bar. Note that the self-to-self annotation is always equivalent to the number of genes present in the original GenBank record.

Mentions: To validate the annotations produced by Plann, we reciprocally annotated plastomes of taxa at varying phylogenetic distances. The reference GenBank records used were NC_024735.1 (Populus balsamifera), NC_009143.1 (P. trichocarpa), NC_024734.1 (P. fremontii), NC_024681.1 (Salix interior), and NC_012224.1 (Jatropha curcas). This analysis can be found in the repository at test/analysis.sh. The comparative results are presented in Fig. 1. Nearly all features were successfully annotated within a genus. Even for a distantly related pair of taxa, Plann was able to identify nearly 70% of the features present in the annotation.


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

Huang DI, Cronk QC - Appl Plant Sci (2015)

For each GenBank record along the x-axis, the number of genes annotated by Plann for the raw plastome sequence is represented by a bar. Note that the self-to-self annotation is always equivalent to the number of genes present in the original GenBank record.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542940&req=5

fig1: For each GenBank record along the x-axis, the number of genes annotated by Plann for the raw plastome sequence is represented by a bar. Note that the self-to-self annotation is always equivalent to the number of genes present in the original GenBank record.
Mentions: To validate the annotations produced by Plann, we reciprocally annotated plastomes of taxa at varying phylogenetic distances. The reference GenBank records used were NC_024735.1 (Populus balsamifera), NC_009143.1 (P. trichocarpa), NC_024734.1 (P. fremontii), NC_024681.1 (Salix interior), and NC_012224.1 (Jatropha curcas). This analysis can be found in the repository at test/analysis.sh. The comparative results are presented in Fig. 1. Nearly all features were successfully annotated within a genus. Even for a distantly related pair of taxa, Plann was able to identify nearly 70% of the features present in the annotation.

Bottom Line: Plann's output can be used in the National Center for Biotechnology Information's tbl2asn to create a Sequin file for GenBank submission.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, University of British Columbia, 3529-6270 University Blvd.,Vancouver, British Columbia V6T 1Z4, Canada.

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.

No MeSH data available.