Convert .gbf file to .gbk or .gff

Question

[che.bellaj]

Hi I am a beginner in bioinformatics and I want to know how I can convert .gbf file to .gbk or gff or gtf file?

[iraun]

• Genbank To Gtf Converter
• Any tools converting Genbank format to GFF3 format?

[cyril-cros]

Quick note:

• .gbf and .gbk are written in a rather verbose format which gives a lot of information about genes (including source of publication,sequence, the animal species and strain).
• .gff and .gtf are tab-separated files representing the position of genes and transcripts (exons, introns, UTRs) in a reference genome (chromosome, dna strand, position for each element : it is an annotation of the genome)

You won't be able to do a lossless conversion I think. Such files usually have an identifier for each entry which gives you the name of the relevant gene. I suggest you download the proper reference annotation as a .gtf/.gff, keep your files apart, and do some parsing on the identifier to match records in each file.

[che.bellaj]

I can convert .gbk to gff even I do a lossless conversion I think

[cyril-cros]

My bad, you can add all sort of data to the attribute field of a GTF file. Might be unwieldy though, depending on the number of attributes / number of genes you consider. Especially fasta sequences...