Hi !
I was wondering what were the differences between those three files :
[https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/]
- *_rna.fna.gz : FASTA format of accessioned RNA products annotated on the genome assembly; Provided for RefSeq assemblies as relevant (Note, RNA and mRNA products are not instantiated as a separate accessioned record in GenBank and are provided for some RefSeq genomes, most notably the eukaryotes.).
- *_rna.gbff.gz : GenBank flat file format of RNA products annotated on the genome assembly; Provided for RefSeq assemblies as relevant.
- *_rna_from_genomic.fna.gz : FASTA format of the nucleotide sequences corresponding to all RNA features annotated on the assembly, based on the genome sequence.
I would like to find a gene that may have a STOP codon stopping the traduction and i don't really know in which file should I look for it ?
Thank you a lot for your help,
Maxime Policarpo
In essence, all three files have the same information, in a different format. However, there are some differences, in the file *_rna. fna. gz you can find the basic information of the sequence and the sequence of nucleotides. In the file *_rna. gbff. gz, you have the nucleotide sequence but it contains some extra information such as the name or access number of the gene, ncRNA, exons and variations. The file *_rna_from_genomic. fna. gz contains the nucleotide sequence based on genome sequence, but this file cannot always be found on the NCBI site. My advice is, use the *_rna file. gbff. gz and if you are lucky the STOP codon annotation should be done. Or if you are going to do the stop codon search yourself, it is easier to use the file *_rna. fna. gz. I add an image where you can see the differences between the formats *_rna. fna. gz and *_rna. gbff. gz.
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