Question: Change Scaffold Orientation
1
gravatar for bioLife
7.3 years ago by
bioLife50
Sweden
bioLife50 wrote:

There is a genome in unoriented and unorder scaffolds. I am interested in a specific area of the genome. Therefore I managed to align the scaffolds to a closely related species and I got an idea about the orientation of the scaffolds.

Do you know any way to change the orientation inside the genbank file of those scaffolds? In order to upload it later to a genome viewer such as Artemis?

Any help please. Thanks a lot.

eg. is there any way to merge the scaffolds and add one CDS next to the other, in the correct way? In biopython?

genbank scaffolding • 2.7k views
ADD COMMENTlink modified 7.3 years ago by Peter5.9k • written 7.3 years ago by bioLife50

You can try Mauve contig mover option http://gel.ahabs.wisc.edu/mauve/

ADD REPLYlink written 7.3 years ago by HG1.1k

yes i tried mauve, this is the one which I used to align the scaffolds. But then I need the .gbk file to upload it the genome browser. The mauve does not seem to output a gbk file or simiar. Any idea for that?

ADD REPLYlink modified 7.3 years ago • written 7.3 years ago by bioLife50

There is a very similar thread on SEQanswers http://seqanswers.com/forums/showthread.php?t=32828

ADD REPLYlink written 7.3 years ago by Peter5.9k
1
gravatar for Peter
7.3 years ago by
Peter5.9k
Scotland, UK
Peter5.9k wrote:

In Biopython, something like this should work

from Bio import SeqIO
my_record = SeqIO.read("input.gbk", "genbank")
reversed_record = my_record.reverse_complement(id="new_id", ...)
SeqIO.write(reversed_record, "output.gbk", "genbank")

The tricky part is deciding which of the annotations like name etc should be kept or replaced.

ADD COMMENTlink written 7.3 years ago by Peter5.9k

this works fine, thanks a lot.

ADD REPLYlink written 7.2 years ago by bioLife50
0
gravatar for cts
7.3 years ago by
cts1.6k
Pasadena
cts1.6k wrote:

You could try Pagit from the Sanger institute. It contains a program called abacas that does contig ordering using mummer and gives you a fasta file of the ordered scaffolds and a genbank like feature table of how the contigs were ordered.

ADD COMMENTlink written 7.3 years ago by cts1.6k

Thank you for the answer. I will try it out. Do you know if there is any tool that reverses the order of the feature coordinates in a gbk file? Is that doable in biopython?

ADD REPLYlink written 7.3 years ago by bioLife50

My guess is it is doable in biopython, how easy it will be to do is another matter. I've never delved into the features/annotations API that much, so I really don't know

ADD REPLYlink written 7.3 years ago by cts1.6k
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