order scaffolds

[pmgr]

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.

I want to visualize it in a genome browser in the correct order.
Any idea how to modify the orientation inside the genbank file of those scaffolds?

Any help please`?

[SES]

The ABACUS program was designed for this purpose and I have found it to work quite well. ABACUS is a part of the PAGIT pipeline, which includes other programs that you may find useful.

[maubp]

Here's a duplicate question on BioStars,
http://www.biostars.org/p/79104/

Here's an older BioPerl answer http://www.biostars.org/p/43236/