Abstract
Background A genome browser transition utility designed in our lab, FPD2GB2 (Fungal Project Database to GBrowse 2), exports data from a custom database used by the Fungal Endophytes Genome Project [1,2]. Designed as a collection of scripts, FPD2GB2 outputs the contents of a locally developed genome annotation database into the standard GFF3 format, allowing for bulk import of data into the GBrowse2 genome browser [3]. In short, FPD2GB2 is a collection of scripts designed to export data encoded in the Fungal Project Database format into a format which can be easily imported into GBrowse 2, namely GFF3.
Highlights
A genome browser transition utility designed in our lab, FPD2GB2 (Fungal Project Database to GBrowse 2), exports data from a custom database used by the Fungal Endophytes Genome Project [1,2]
Adding a data validator as part of the FPD2GB2 script collection allows for independent verification of the quality and soundness of the GFF3 files being imported into a production GBrowse2 environment
We measure the accuracy of the output by comparing the features listed in the GFF3 files to the contents of the original database
Summary
A genome browser transition utility designed in our lab, FPD2GB2 (Fungal Project Database to GBrowse 2), exports data from a custom database used by the Fungal Endophytes Genome Project [1,2]. Materials and methods Any application which converts between data formats should ensure the completeness and accuracy of the output produced by FPD2GB2. Adding a data validator as part of the FPD2GB2 script collection allows for independent verification of the quality and soundness of the GFF3 files being imported into a production GBrowse2 environment. We measure the accuracy of the output by comparing the features listed in the GFF3 files to the contents of the original database.
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