Hi everyone,
Experimentalist trying to get introduced to some basic bioinformatics, I've recently started to use R Bioconductor, but getting quite lost yet.
I'm would like to use this new skills to convert a Genebank file (.gbk) downloaded from ncbi, to a multifasta file containing all genes, nucleotides (.ffn), so it would be great if any now can give me the exact script I have to use:
1) Import the .gb file
2) transform .bg to .ffn
3) Export .ffn to tab file (so I can open it using textedit)
I know is kind of very basics, but thank you in advance.
Cristina
Hi Cristina,
Unfortunately I think there is no easy way to do this in R. I might also be wrong and someone can correct me.
I would use biopython or bioperl for this. With biopython I can help you.
br,
Antti
I also think Perl an Python already have good scripts for this: http://stackoverflow.com/questions/6336853/convert-genbank-flatfiles-to-fasta GeneR seems to understand both FASTA and GenBank formats, so that should be a possibility if you really need to use R: http://bioconductor.wustl.edu/bioc/vignettes/GeneR/inst/doc/GeneR.pdf
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