It looks like that last point is most likely, but unless I missed something it looks like Prokka is already doing that for you. pull out the coding sequence of each gene and translate it into its corresponding peptide sequence?.pull out the sequence corresponding to every gene? More common, but since you want to do proteomics you're probably not interested in promoters or introns (if either of these are annotated in your GFF file).pull out the sequence corresponding to every GFF record? Usually not helpful, since many records are children of other records.It can be done in a hundred subtly different ways, and most of these programs are designed for a single narrow use case. Many, many scientists have written throwaway programs to do this type of task. There are many ways to extract sequences from a Fasta file that has been annotated with a GFF file. So in this context, a " tool that converts gff to annotated fasta" doesn't make sense since it's an underdefined task. The GFF file labels that interval as a gene or transposable element or transcription factor binding site or whatever genomic feature you're interested in. Each record in the GFF file specifies a sequence (such as chr6 or scaffold1985) and an interval (such as 19920557-19997344 or 2488-2489). GFF files are designed to hold annotations corresponding to sequences, most often genomic sequences such as chromosomes or (if it's a draft genome assembly) scaffolds or contigs.The information that should be the defline of a FASTA record depends primarily on the tool(s) used to produce and analyze the data. There are no strict requirements, although there are many common conventions. The "defline" (header) of each record may include some unique identifiers or descriptive metadata. FASTA files are designed to hold nucleotide or amino acid sequences.This is not an uncommon question / request, but perhaps a crash course refresher on file formats would provide some valuable context. Is there any tool that converts gff to annotated fasta?
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