User GuidesSnapGene Importing and ExportingImport Features from a GTF, GFF3, or BED File

Import Features from a GTF, GFF3, or BED File

How do I import features into a SnapGene file from a GTF, GFF3, or BED file?

GTF, GFF3, and BED are standard files formats for storing feature information in plain text.

GFF stands for Generic Feature Format. A GFF3 file describes features with coordinates corresponding to a specific reference sequence. See this link for more information.

GTF is similar to GFF3 and is sometimes referred to as GFF2.5. See this link for more information.

BED stands for Browser Extensible Data. This format was developed for the human genome project. See this link for more information.

A GTF, GFF3, or BED file can describe features for multiple reference sequences. Note that SnapGene cannot currently import multi-sequence GTF, GFF3, or BED files.

A GTF or GFF3 file may include one or more reference sequences as embedded FASTA data. Note that SnapGene cannot use a FASTA sequence embedded in GTF or GFF3 files as a reference.

In most cases a GFF3 file is accompanied by a separate reference file in FASTA format.

Import or Open a Reference Sequence

Finder

Import or open a reference sequence. For example, drag a reference sequence file onto the SnapGene launch window, or click File → Open to locate and import the reference sequence file.

You may need to specify whether the sequence should be linear or circular.

Import the GFF3, GTF, or BED File

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Ensure that the reference sequence is the front SnapGene window, then click Features → Import Features → Import Features from a [BED, GFF3, or GTF] File... .

Use the Browse button to locate and load the feature file. Click OK to import the feature information into the reference sequence file.

The features described in the GTF, GFF3, or BED file will be displayed on the reference sequence in Map and Sequence views, and will be listed in Features view. Click File → Save to save the annotated sequence as a SnapGene file.

Creating Feature Files for Use in SnapGene

This section provides information and example files for advanced users when creating GFF3, GTF or BED feature files for import into SnapGene.

Creating GFF3 Files

The attached zip archive contains a text file, called GFF3.txt, that details the SnapGene GFF3 import specification and a description of example files. The archive contains example GFF3 files and reference DNA and Protein sequence files.

Download and unzip the archive to learn about creating GFF3 files that are compatible with SnapGene.

See also, http://gmod.org/wiki/GFF3 for further information about GFF3 format.

Creating GTF Files

The attached zip archive contains a text file, called GTF.txt, that details the SnapGene GTF import specification and a description of example files. The archive contains an example GTF  file and a reference DNA sequence file.

Download and unzip the archive to learn about creating GTF  files that are compatible with SnapGene.

See also, https://mblab.wustl.edu/GTF22.html, for further information about GTF format.

Creating BED Files

The attached zip archive contains a text file, called BED.txt, that details the SnapGene BED import specification and a description of  example files. The archive also contains an example BED sample file and a reference DNA sequence file.

Download and unzip the archive to learn about creating BED files that are compatible with SnapGene.

See also, https://ensembl.org/info/website/upload/bed.html for further information about BED format.