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GFF tools


May 11, 2011: Abstract about the GFF tools accepted for a poster presentation at BOSC 2011.


A collection of tools gives a better understanding about data in a Generic feature format Version 3. The programs are available at our Galaxy server.

The stand-alone versions of each tool along with Galaxy wrappers are available here.


Python, Perl



The tools in the first section validate the GFF file and returns a detailed report on the file contents. They are:

  1. Examine
  2. FeatureScan
  3. Comprehensive GFF3 Validator
  4. MergeLoci

The second section mainly deals with converting between GTF, BED, GenBank and GFF3 formats, Which includes:

  1. GTF_to_GFF3
  2. GFF3_to_GTF
  3. BED_to_GFF3
  4. GFF3_to_BED
  5. GenBank_to_GFF3

Detailed description and usage

a(1). Examine

Provides the features(gene, mRNA, UTR's, exon, CDS etc) relationship based on their identifier mapping in a genome annotation file.

python example.gff3

a(2). FeatureScan

Provides an overview of available contig identifiers, sources and feature types and their corresponding counts from a given genome annotation file.

python example.gff3

a(3). Comprehensive GFF3 Validator

Provides a comprehensive scanning over genome annotation file, for example: Consistency check for contig ID present in provided genome sequence file (FASTA) and GFF3.

python example.gff3

a(4). MergeLoci

MergeLoci will be able to merge several transcripts from single loci to a main feature instead of several features.

python example.gff3

b(1). GTF_to_GFF3

Converts data from Gene Transfer Format to a valid Generic Feature Format Version 3.

python -q example.gtf -o example.gff3

b(2). GFF3_to_GTF

Converts data from Generic Feature Format Version 3 to Gene Transfer Format

perl example.gff3 example.gtf

b(3). BED_to_GFF3

Converts data from a 12 column UCSC wiggle Browser Extensible Data (BED) format to Generic Feature Format Version 3.

python -q example.bed -o example.gff3

b(4). GFF3_to_BED

Converts data from Generic Feature Format Version 3 (GFF3) to UCSC wiggle 12 column Browser Extensible Data.

python -q example.gff3 -o example.bed

b(5). GenBank_to_GFF3

Converts annotations in GenBank format to Generic Feature Format Version 3 (GFF3).

perl -f GenBank example.gbk -out stdout > example.gff3

More information about each tool can be found at Galaxy tool page. Questions/Comments/Suggestions, I can be reached at

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