How to orient and order a bundle of sequences based on a reference sequence

Question

[Yongjie Zhang]

Hello,

I have dozens of contig sequences representing mitochondral fragments of a species, and want to orient and order these sequences by refering to a reference mitochondrial genome sequence. I used to do it by hand, but do you know an easy way to do this? Any programs or scripts?

Thanks,

Yongjie

[Pierre Lindenbaum]

blast and grep the orientation

[Yongjie Zhang]

Dear Pierre, Could you please give more details?