[maker-devel] RepeatMasker Species Option

[Reith, Michael]

There are also a couple of utilities that come with RepeatMasker (in the
util directory) - queryRepeatDatabase.pl and queryTaxonomyDatabase.pl -
that are useful for seeing what species are in Repbase and their higher
order taxa.  Run them without options to get the usage.  The
repeatmasker.help file also gives some useful basic info on species
usage for RepeatMasker.  As a last resort, you could also do a find on
taxonomy.dat for your organism of interest or a related species.

 

Cheers,

Mike

 

________________________________

From: maker-devel-bounces at yandell-lab.org
[mailto:maker-devel-bounces at yandell-lab.org] On Behalf Of Carson Holt
Sent: October 22, 2009 9:40 PM
To: Daniel Standage; MAKER Mailing List
Subject: Re: [maker-devel] RepeatMasker Species Option

 

RepeatMasker uses NCBI phylogenetic names and other common names.  You
can use specific organism names like 'Homo sapiens', or group names like
'mammals', 'vertebrates', or 'chordata'.  There are actually over 5,000
accepted terms.  Try using 'fungi' as your species name.  That should
gather together all repeats from all fungal genomes in RepBase into the
search space.

Carson

On 10/22/09 4:35 PM, "Daniel Standage" <byuhobbes at gmail.com> wrote:

I spent a bit of time today trying to find an exhaustive list of species
options for RepeatMasker, but after re-reading the help statement, it
looks like the species options available to you depend on your repeat
database. Does this mean I have to scrape the database files to see what
species are included? Any suggestions about how to get a list of
available species options?  FYI, we want to run maker with a fungal
genome.

Thanks!

Daniel Standage
Plant Genetics Lab
Brigham Young University

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