Introduction

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.

Requirements

Python, Perl

Contents

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 gff_idmapper.py 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 gff_featurescan.py 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 comprehensive_check.py 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 gff_mergeloci.py example.gff3

b(1). GTF_to_GFF3

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

python gtf_to_gff3_converter.py -q example.gtf -o example.gff3

b(2). GFF3_to_GTF

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

perl gff3_to_gtf_converter.pl 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 bed_to_gff3_converter.py -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 gff3_to_bed_converter.py -q example.gff3 -o example.bed

b(5). GenBank_to_GFF3

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

perl genbank2gff3.pl -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 vipin.ts@tue.mpg.de