You use EMBOSS union like this:

% union -sequence in.gbk -outseq out.gbk -osformat genbank -feature -auto

You can view this in Artemis

% art out.gbk

Hi Pieter, You can try Geneious. Free and pretty powerful suite of software.

http://www.geneious.com

I believe Artemis needs a single Genbank record, so it ignores all the rest after the first. The EMBOSS command/utility called 'union' will concatenate Genbank files. Be sure to use the '-features Y' option to force it to include the features from all the files in the output; by default it won't. One caveat - I've used this for concatenating multiple files. Not sure what it does with a multi-record file.

It is also possible to programmatically read in the multi-record Genbank file using BioPython (or BioPerl) and then join all the records into 1 and output that as a single Genbank file.

Geneious doesn't seem to be free.

EMBOSS-union also only reads the first contig.

Does anyone has a working Python script to concatenate multiple records in a genbank file?

indentation will be off (used dots for indents), so will need to fix it, but this should work:

from Bio import SeqIO

merged_rec = ''

infile = "multi-rec.gbk"

for rec in SeqIO.parse(open(infile,"r"), "genbank") :

....merged_rec += rec

....# you could insert a spacer if needed

....# merged_rec += rec + ("N" * 50)

merged_rec.id = "mergedseq"

merged_rec.description = "merged seq"

SeqIO.write(merged_rec, "merged.gbk", "genbank")

Excellent, works like a charm.