11
votes
Accepted
Can exons be located outside of the coding sequence?
Yes, of course. Exons are not limited to the protein coding regions. Many UTRs are in exons. In fact, you even have various cases of UTRs being multiple exons, and being spliced.
What is strange in ...
- 9,662
8
votes
Can exons be located outside of the coding sequence?
Those are the untranslated regions (UTRs). All mRNAs have a 5' UTR and a 3' UTR. These give the ribosome something to grab onto and often contain important regulatory sites such as miRNA target sites.
- 1,749
8
votes
How to convert BED to GFF3
To answer the question as asked, for people googling.
For BED6, in python:
...
- 3,301
8
votes
Accepted
How GFF3 attributes (9th column) varies from one gene prediction algorithm to another
The first place to start is the GFF3 specification. This is the official word on what is and is not allowed in a GFF3 file. For example, users can define arbitrary attribute keys, so long as they do ...
- 5,060
8
votes
Accepted
How to convert BED to GFF3
Galaxy has API and API-consuming libraries (such as BioBlend) that will allow you to interactively script against it without opening the graphical interface at all.
However you can also take almost ...
- 196
6
votes
Accepted
How to extract / convert gff3 CDS sequences to multifasta
I like bedtools getfasta. My typical option set is bedtools getfasta -fi <reference> -bed <gff_file> -name -s. Be ...
- 2,574
5
votes
Accepted
In GFF3, annotating more than one protein-coding gene (i.e. polycistronic) contained in a eukaryotic mRNA
The GFF3 file format specification doesn't care where annotations are described in the file, although it can make some things easier if the annotations are ordered by the start position:
...
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5
votes
Accepted
5
votes
Accepted
What kind of "gff" format does bioawk parse?
I would consider the description there a bug. The filter is actually the strand, strand is the frame, ...
- 19.6k
5
votes
How to convert BED to GFF3
To convert BAM to GTF, which is the best way to get a file to compare with cuffcompare:
...
- 3,301
4
votes
How to extract / convert gff3 CDS sequences to multifasta
The gffread utility in Cufflinks package might be interesting for you. To generate a multi-fasta file with nucleotide sequences from your GFF file, then you can try:
...
- 2,676
4
votes
How to convert BED to GFF3
Bioconductor makes this so easy. It does the coordinate conversion on import.
...
- 1,573
4
votes
Annotation format design
I quite like BED and GFF3 (I don't like GTF/GFF2, though). As text-based formats, I don't think they leave us much room for improvement. Anyway, if you want a new format, here is one. The following is ...
- 6,485
4
votes
Annotation format design
The problem is that GFF, fundamentally, is a relational format: it provides tags that relate individual rows via one-to-many relationships (e.g. gene–exon). This indirectly highlights the second ...
- 4,845
4
votes
Annotation format design
Presuming we consider "human readable", "easily parsable", and "quickly queryable" to be objectively good qualities (and if not, I worry for the future):
Text-based: It's absurdly common to want to ...
- 19.6k
4
votes
Transferring genomic features on new coordinates
I think the standard way of doing this is to make a chain file, then use it to do a liftOver of the annotations:
...
- 1,816
4
votes
Infer missing UTR features in GFF3 file
Among other things, the canon-gff3 program in the AEGeAn Toolkit infers and prints missing features like UTRs.
...
- 5,060
4
votes
Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3
The three # are used for splitting group of features that belong together, e.g. a transcript and it's exons. Sometimes you see with a blank line instead of the <...
- 1,342
4
votes
Accepted
Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3
There are some good answers so far, but I don't think any of them fully communicate the significance of the ### directive. The GFF3 specification states:
This ...
- 5,060
3
votes
Accepted
Infer missing UTR features in GFF3 file
Annoyingly, you can load such a GFF3 file into R (using the GenomicFeatures package) and access the UTRs, but they don't then get saved if you use the export ...
- 19.6k
3
votes
Accepted
Does Prokka or gff3 change the sequence / subject ID of fasta files?
Prokka is an annotation tool. It takes your contigs file with fasta headers >NODE_108...and searchs for ORFs and their putative functions. Prokka produces ...
- 955
3
votes
Accepted
How to dump genes from GenBank in GFF3 format?
Turns out you can just grab the GFF3 from the NCBI's FTP site!
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/003/195/GCA_000003195.3_Sorghum_bicolor_NCBIv3/
See:
https://www.ncbi.nlm.nih.gov/...
- 602
3
votes
How to extract / convert gff3 CDS sequences to multifasta
Using python and this GFF parser that mimics Biopython's SeqIO parsers:
...
- 967
3
votes
Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3
As others have stated, those are just there to separate the entries for easier parsing. They enable you to do nifty tricks like:
...
- 9,662
3
votes
Existing tool for converting gff3 to genbank (gbk)
I believe seqret is already the simplest approach. If you install the emboss command line utility, genome (file) sizes will not be a problem. You can even install ...
- 178
3
votes
Accepted
Edit end column in GFF3 file
That's what awk excels at! Simply set the input (-F '\t') and output (-v OFS='\t') record field separators to tab, and add 30 to ...
- 9,662
3
votes
Accepted
How to wget a gff from NCBI database?
my suggestion would be to go via the assembly page.
For your example link, I would
Click the link to the BioProject: PRJNA164
On the right side, under "Related information" choose the ...
2
votes
How to convert BED to GFF3
If anybody needs a simple bed to gff converter, simple in the sense that only takes a bed with a single type of feature, lets say peaks and translate it to GFF I recently wrote this, is Bash and as ...
2
votes
How to convert BED to GFF3
I recently developed bed2gff to quickly convert .bed files to a gff3 format, a tool written in Rust. Could be of help here!
2
votes
How to extract / convert gff3 CDS sequences to multifasta
The xtractore program from the AEGeAn Toolkit was designed for this type of use case. Just set --type=CDS.
...
- 5,060
Only top scored, non community-wiki answers of a minimum length are eligible