Jan 09, 2019
- 1Freie Universität Berlin
External link: https://www.biorxiv.org/content/early/2018/10/05/435644
Protocol Citation: Michael Grünstäudl 2019. Usage of EMBL2checklists. protocols.io https://dx.doi.org/10.17504/protocols.io.v6me9c6
Manuscript citation:
Gruenstaeudl M., Hartmaring Y. (2018). EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA. bioRxiv 435644; doi: https://doi.org/10.1101/435644
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: December 05, 2018
Last Modified: January 09, 2019
Protocol Integer ID: 18349
Keywords: bioinformatics, DNA sequence submission, ENA, European Nucleotide Archive, plant DNA barcoding, plant systematics, Python, sequence database, software tool, Webin
Abstract
The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant and fungal DNA barcoding. A Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called "checklists") for a subsequent upload to the annotated sequence section of the European Nucleotide Archive (ENA). The package, titled "EMBL2checklists", automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates output that can be uploaded via the interactive Webin submission system of ENA. Here, we present a step-by-step protocol of the bioinformatic steps necessary to generate submission-ready checklist files from raw DNA sequence data and associated metadata via EMBL2checklists.
Attachments
Annotation of DNA sequences
Add sequence features and feature qualifiers to each DNA sequence using INSDC-compatible feature table keywords.
Use any of the following software tools:
Software
Geneious
NAME
Kearse et al. (2012) Geneious Basic: An integrated and extendable desktop software platform for ... Bioinformatics 28: 1647-1649
DEVELOPER
Geneious is among the most efficient and best-documented tools to adding sequence features and feature qualifiers to DNA sequences. For more information regarding the automatic annotation of sequences with Geneious, see the following video tutorial on Youtube:
Software
Artemis
NAME
Rutherford et al. (2000) Artemis: Sequence visualization and annotation. Bioinformatics 16: 944--945
DEVELOPER
Software
DnaSP
NAME
Rozas et al. (2017) DnaSP v6: DNA Sequence Polymorphism Analysis of Large Datasets. Mol. Biol. Evol. 34: 3299-3302
DEVELOPER
For exporting annotated DNA sequences as GenBank- or EMBL-formatted flat files, see pages 44 to 46 of the user manual of DnaSP v.6.12.
Saving sequences as flat file
Save multiple DNA sequences of the same barcoding marker as an single, multi-sequence flat file in EMBL or GenBank format. Use any of the following software tools:
Software
Geneious
NAME
Kearse et al. (2012) Geneious Basic: An integrated and extendable desktop software platform for ... Bioinformatics 28: 1647-1649
DEVELOPER
Geneious is among the most efficient and best-documented tools to export annotated DNA sequences as a GenBank flat file format.
Software
Artemis
NAME
Rutherford et al. (2000) Artemis: Sequence visualization and annotation. Bioinformatics 16: 944--945
DEVELOPER
Software
DnaSP
NAME
Rozas et al. (2017) DnaSP v6: DNA Sequence Polymorphism Analysis of Large Datasets. Mol. Biol. Evol. 34: 3299-3302
DEVELOPER
For exporting annotated DNA sequences as GenBank- or EMBL-formatted flat files, see page 93 of the user manual of DnaSP v.6.12.
Validation of flat file
Test the validity of the file format, the feature table syntax or the taxonomic status of organism names, among other aspects, using one of two software tools.
For validation of EMBL-formatted flat files, use:
Software
EMBL flat file validator
NAME
Command
Command to validate the format and content of an EMBL-formatted flat file (which is used as input to EMBL2checklists in the subsequent protocol step) via the EMBL flat file validator.
For validation of GenBank-formatted flat files, use:
Software
SBOL Validator
NAME
Installation of EMBL2checklists
It is recommended that you install EMBL2checklists via pip (i.e., the recommended installer of the Python Package Index). On Linux and MacOS, this can be achieved via the following command:
Command
Command to install EMBL2checklists via the default Python installer.
Conversion from flat file to checklist
Convert the EMBL- or GenBank-formatted flat file into the Webin checklist file format using the software:
Software
EMBL2checklists
NAME
Command
Command to run EMBL2checklists on an example dataset provided as part of the Python package.
Video tutorial of the correct execution of EMBL2checklists via the command-line on an example dataset provided as part of the Python package.
Command
Command to run EMBL2checklists on an example dataset provided as part of the Python package.
Video tutorial of the correct execution of EMBL2checklists via the GUI on an example dataset provided as part of the Python package.
Upload checklist to ENA
Upload the resulting checklist to the sequence section of ENA using the interactive route of the Webin submission system.