Abstract
GTF (Gene Transfer Format) and GFF (General Feature Format) are popular file formats used by bioinformatics programs to represent and exchange information about various genomic features, such as gene and transcript locations and structure. GffRead and GffCompare are open source programs that provide extensive and efficient solutions to manipulate files in a GTF or GFF format. While GffRead can convert, sort, filter, transform, or cluster genomic features, GffCompare can be used to compare and merge different gene annotations. Availability and implementation: GFF utilities are implemented in C++ for Linux and OS X and released as open source under an MIT license ( https://github.com/gpertea/gffread, https://github.com/gpertea/gffcompare).
Highlights
Many biomedical research applications employ pipelines to systematically analyze the gene content in a genome
Such tools usually exchange and employ information about genes, transcripts or other genomic features in a tab-delimited text file format commonly known as GFF (General Feature Format)
Where provides the sequence name of the feature’s location, is the program that generated that feature, gives the actual type of the feature, and are the start and end coordinates of the feature on the sequence, is a floating-point number that represents the score attributed to that feature, gives the strand of the feature on the sequence, is used for a coding feature to indicate where the codon begins relative to the 5’ end, and specify additional characteristics for the feature that depend on the specific version of the GFF format used and usually include at least a unique identifier for that feature
Summary
Any reports and responses or comments on the article can be found at the end of the article. This new version contains minor text edits to address observed typos and clarify the meaning of some wordings as suggested by the reviewers. Any further responses from the reviewers can be found at the end of the article
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