Identifying marker locations on a reference genome

[Dave Yarmosh]

Is there a way to identify where on a reference genome a specific marker belongs? Markers are named by protein name, which can be traced back to a gene, but because the marker is a subset of the marker family is a subset of the protein - this is ultimately nonspecific.
I know that the markers, being the result of MSA of consensus sequences of proteins, may not perfectly align to a given genome (even if that species/strain/whatever was used to generate the marker), but can this be done?

Could I convert the markers into a BLAST DB and tblastn a given genome against that?

Does this make sense? If so, thoughts? Otherwise, feel free to ask for clarification.

Dave

[Dave Yarmosh]

Scratch tblastn in favor of blastx.
Dave

[Eric Franzosa]

Hi Dave,

If you want to know the precise location of the marker inside a genome (especially a new genome), I would probably reverse the search you suggested: i.e. index the genome and then search the marker against genome database.

Thanks,

Eric

On Thu, Jan 11, 2018 at 10:20 AM, Dave Yarmosh <yar...@gmail.com> wrote:

Scratch tblastn in favor of blastx.
Dave

On Thursday, January 11, 2018 at 10:15:22 AM UTC-5, Dave Yarmosh wrote:

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