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
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 single stranded or doubled stranded, and linear or circular.
The reference is now ready for annotation of features specified in a GFF3, GTF or BED file.
Import the GFF3, GTF, or BED File
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 who want to create 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 provides a description of example feature 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 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 provides a description of example feature 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 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 provides a description of example feature 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 https://ensembl.org/info/website/upload/bed.html for further information about BED format.