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Old 03-28-2011, 02:17 AM   #1
NicoBxl
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Default multiple gbk file

Hi,

Is it possible to merge multiple gbk file. I've one gbk per chromosome and I want to have one gbk file for the whome genome (it's for Bos Taurus for info )

Thanks,

N.
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Old 03-28-2011, 07:01 AM   #2
krobison
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Standard Genbank format requires a line with just // between entries (which your entries should end with), but whether the tools you are using will handle that can only be found by testing.
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Old 03-28-2011, 08:51 AM   #3
kokonech
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You can use UGENE extension Workflow Designer.

I've attached a workflow schema that allows to input multiple genbank files and merge them into single one.

Install UGENE and open the schema file. Then set input parameters for Read Sequence element - it would be your multiple files. Don't use iterations, since you don't need any specific behavior for each file. Finally set output file for Write Genbank element and run schema.

Hope that helps,
Konstantin
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File Type: gz merge_sequences.uwl.gz (3.0 KB, 168 views)
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Old 03-28-2011, 10:16 AM   #4
maubp
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Quote:
Originally Posted by NicoBxl View Post
Hi,

Is it possible to merge multiple gbk file. I've one gbk per chromosome and I want to have one gbk file for the whome genome (it's for Bos Taurus for info )

Thanks,

N.
Yes, but as krobison said, some tools will only expect one record per file.

The easiest way to do this at the command line is with the cat command. e.g.

Code:
cat file1.gbk file2.gbk file3.gbk > merged.gbk
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