I need to be able to easily change between GFF/GTF + reference to either EMBL and GenBank formats, and vice versa. Are there are any frequently used tools for accomplishing this, or should I script something myself?
Generating an EMBL-Bank style entry from a fasta sequence and a GFF feature table:
seqret -sequence aj242600.fasta -feature -fformat gff -fopenfile aj242600.gff -osformat embl -auto
Alternatively to get a GenBank style entry:
seqret -sequence aj242600.fasta -feature -fformat gff -fopenfile aj242600.gff -osformat genbank -auto
To go the other way and get the sequence in fasta format and the features as GFF use something like:
seqret -sformat embl -sequence aj242600.dat -feature -osformat fasta -offormat gff -auto
Please note that since these are starting from sequence plus features they do not create a full EMBL-Bank or GenBank style entry, since this requires additional information, such as references, not available in the source data.