Question: Available software for checking all species have a 4d site for a particular codon in alignment?
gravatar for RoryC
4.7 years ago by
Uppsala, Sweden
RoryC30 wrote:

Hi guys,

I have a whole genome alignment for many species and a file containing coding sequence coordinates for one focal species, which I will use to extract 4d sites from the alignment and produce a phylogeny. What I would like to check is if what is a 4d site in the focal species actually corresponds in the alignment to 4d sites for each of the other species i.e. for each codon in the focal species which contains a 4d site, check each aligned codon for each species individually to ensure that they also have a 4d site at that position. Does anybody know of any existing software which can check this?

Cheers, Rory

alignment gene genome • 1.4k views
ADD COMMENTlink modified 3.5 years ago by mtollis30 • written 4.7 years ago by RoryC30

Can't you just extract all the 4d sites into a new alignment and then check it column by column with something like sort?

ADD REPLYlink written 4.7 years ago by 5heikki9.0k

Hi, thanks for the suggestion! I could see a way of writing a code for this, but I imagine it would be more complicated than that as you'd have to compare to a codon table to make sure the codon for each specific species has a 4d site in the 3rd position.

ADD REPLYlink written 4.7 years ago by RoryC30

Hi RoryC, I have the same question as you. Have you solved this problem? Could you share the script or software to me? Many thanks in advance.

ADD REPLYlink written 4.1 years ago by haoyan14ioz0
gravatar for mtollis
3.5 years ago by
United States
mtollis30 wrote:

If your focal species is a reference species in your alignment as in one constructed with MULTIZ, and it has available CDS annotations, you should try msa_view from the PHAST package.

ADD COMMENTlink written 3.5 years ago by mtollis30
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