fasta to gff3

Question

[kelishady]

Hi.How to download a GFF3 file? On the other hand, how to convert fasta format to gff3 format?

[Michael]

Dear kelishady, welcome to biostars Unfortunately, it is unclear what you are asking the reason for this being that have not invested the appropriate amount of effort. It is highly appreciated that other users are willing to put their precious time into answering even these kind of questions! However, please remember this rule of thumb: If your question consists of a single sentence, then it is not good enough and you should write more. Please read http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202 for hints on writing good questions.

[finswimmer]

Wow, a publication with 13 authors for something that should be normal. It's a pity that this is necessary.

Answer 1

[Philipp Bayer]

There are numerous sources for gff3 files, it always depends on which organism you work with - Ensembl has many annotations in gff3 files, one example: http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index

I'm not sure I understand your second question. A fasta file contains a whole genome assembly or a set of coding or protein sequences, a gff3 file contains the coordinates of any feature within an assembly (another fasta file). They are usually not interchangeable.