liftover a fasta file

Question

[diviya.smith]

I was wondering if there is an easy way to liftover an entire genome. I want to liftover a fasta file from pantro2 to pantro4 genome positions. There was no ancestral sequence generated for pantro4. Is there an easy way to do this? I think the UCSC liftover will be extremely slow for regions. Dont want to code this myself if someone else has already done it before.

[Cyriac Kandoth]

liftover seems inappropriate for what you're trying to do. It simply maps equivalent loci in one genome to another, and cannot handle sequence data like in FASTA files.

Answer 1

[PoGibas]

Use UCSC blat to map sequence to pantro4.

[diviya.smith]

Thanks for the suggestion. I tried BLAT but I think it has a max sequence limit on the online version - perhaps that can be changed for running it locally. Is there any other option? BLAT is not applicable for my analysis as I want to remap the coordinates of the ancestral sequence and so I dont really want to match orthologous regions on the two sequences

• Sequence chr22 is 34894545 letters long (max is 75000), skipping