Hello every one.
Hope you can help me. The task seems to be rather easy. I have a set of bacterial draft genomes in .gbk format and I want to used them as input into KEGG Automatic Annotation Server to assign KO numbers and extract main pathways. The problem is that the system require to input multi-fasta files.
I've already tried to find some tools by web searches but couldn't' found a proper one yet. So if you know any tool that would allow me to input large data sets (>5Mb) to convert genbank to fasta files would be a great help.
Thank you in advance.
Cristina
What kind of operating system (OS) are you using? If you are comfortable with Linux, you can try to run SeqIO of Biophyton. In fact, it runs on many OSs. Here is some information on this: http://www.biopython.org/wiki/SeqIO
In order to convert the gbk. files to fasta, this should then work:
from Bio import SeqIO
SeqIO.convert("NC_number.gbk", "genbank", "NC_number_converted.fna", "fasta")
I happened to find an online converter, but I am not sure if it would work with relatively big files. Here: http://www.dnabaser.com/download/GBK-converter/
Good luck!
You can do this via ReadSeq command line tool (http://iubio.bio.indiana.edu/soft/molbio/readseq/java/). There is also a web-interface at EBI for ReadSeq: http://www.ebi.ac.uk/Tools/sfc/readseq/
May be a little too late for responding. Just use Seqret command in Emboss. By far the easiest way to deal with this conversion.
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