How can I change the reference genome in a multiple alignment (maf format)

Question

[vasilislenis]

Hello everybody,

I want to use some multiple alignments from UCSC but they are built by using human as a reference.

I would like to change the reference genome (from human to cattle) and I was wondering if there is any specific tool that I could use to do that.

Thank you in advance,
Vasilis.

[Phil S.]

If I understand you correctly, you want to change the reference sequence the alignment is made to. So, this would change the whole alignment. So what you can just do is use the sequences you need and calculate a new alignment using cattle as ref.

[vasilislenis]

Yes, correct. I know that the whole alignment will change and practically I will loose some alignments but at the moment it doesn't bother me. I can sacrifice to loose some alignments for my purpose than to rerun all the whole genome pairwise alignments. So, I was wondering if by changing the order of the species (put cattle first) if I could make it. Another thing that I'm thinking is what I should do with the cases that I have more than one cattle chromosome that align in each human chromosome….

[Phil S.]

usually the sequence used as first input (the one at the very top) is the reference, yes... so you can just change it!