About phastCons output

[JT Guan]

Hello Everyone,

I am using phastCons to get conservative elements by inputting human,mouse,rat multiple alignment file, for example chr1.hmr.maf.

And the .bed output is:
chr1 4424 4589 chr1.1-999145.1 43 +
chr1 5434 5511 chr1.1-999145.2 27 +
chr1 6312 6395 chr1.1-999145.3 21 +
chr1 16785 17057 chr1.1-999145.4 104 +
...

The result just specifies every conservative element's location in human chromosome.
But I also want to know every conservative element's location in mouse and rat chromosome.

Does anyone know how to get this kind of result by adding phastCons option or something else?

Thanks in advance for your help

Regards,
Guan

[Vasilis]

Help for identifying conserved sequences

Hello,
I am trying to identify conserved regions among Human, mouse and rat.
I am really new to this field and I need your help.
I want to try with the human chromosome 22 as reference.
I’m starting with the pairwise alignment between human- mouse and human- rat, I’m creating the chains and nets, after that I convert the nets to maf files and finally with MULTIZ I am taking the multiple alignment.
I am thinking to use the phastCons with the final maf file but phastCons gives you the probabilities of each nucleotide to be in a conserved sequence.
I’m thinking to find the coordinates of the nucleotides that have probability more than a threshold (e.g 0.97) and extract the sequences from the ref genome (human).
As final step, I’m thinking to blast these sequences to the mouse and rat whole genomes.
Do you think that this procedure that I’m thinking is ok?
Is there a way phastCons to give me the sequences and not only the probabilities?
Also, and more important, which parameters I must use for phastCons?
Thank you very much I advance.

[milo0615]

Hi JT Guan,

Were you able to use PhastCons to analyze your data? Please let me know. I am currently analyzing a multiple alignment with three plant species.


Thank you,

-Milo

Hello Everyone,

I am using phastCons to get conservative elements by inputting human,mouse,rat multiple alignment file, for example chr1.hmr.maf.

And the .bed output is:
chr1 4424 4589 chr1.1-999145.1 43 +
chr1 5434 5511 chr1.1-999145.2 27 +
chr1 6312 6395 chr1.1-999145.3 21 +
chr1 16785 17057 chr1.1-999145.4 104 +
...

The result just specifies every conservative element's location in human chromosome.
But I also want to know every conservative element's location in mouse and rat chromosome.

Does anyone know how to get this kind of result by adding phastCons option or something else?

Thanks in advance for your help

Regards,
Guan