align specific region of human to panTro6

Question

[biosol]

Hi everyone!

I'm trying to efficiently align a fasta file with a human sequence to panTro6 sequence but I'm not sure on how to avoid the gaps between both species. Are there tools that take these gaps already into account? Thanks in advance for the help!

[Pierre Lindenbaum]

e but I'm not sure on how to avoid the gaps between both species.

what does it mean ? if the sequences are large, there will be gaps. you cannot avoid it.

[biosol]

I would like to eliminate from my human fasta those positions that don't have a match with the panTro fasta.

Answer 1

[JC]

Why do you need to align that? If you have human sequences you can use their coordinates to LiftOver the other genome.

[biosol]

Okey! I hadn't heard about LiftOver, but that's exactly what I need! Thank you so much!

[biosol]

And another question @JC : I have done the lift over and I'm having a look at the sequences with UGene (similar to Bioedit). I see now that a big part of panTro6 sequence is displaced just by 1 or 2 nucleotides in some regions. My next step will be to calculate the divergence between both species, so I'm wondering whether this will affect a lot my results... should I eliminate all those "unmatching" regions from both species?? Or should I add/remove this nucleotides to make the sequences match? Thanks a lot again!

[JC]

To calculate divergence you need to keep only conserved blocks.