List of species in RepeatMasker Tool (species parameter)

Question

[nut_B]

Hi,

I would like to ask some question about RepeatMasker Tool. If i want to know the list of species in these tool and choose species. In the parameter of this tool (as -species ......). So I want to mask repeat fungi, If someone have some suggestion please answer me. Thank you for advance.

For now, I use this command : ./RepeatMasker -species fungi filename.fasta

and about information of my organism is Eukaryote, fungi, ascomycete, Xylaria ,respectively

Answer 1

[Medhat]

You can use this tools queryRepeatDatabase.pl and queryTaxonomyDatabase.pl

  queryRepeatDatabase.pl [-version] [-species <species> |
                                     -stage <stage num> |
                                     -class <class> |
                                     -id <id>]
                                    [-stat]
                                    [-tree]
                                    [-clade]


  A utility script to query the RepeatMasker repeat database.  

  queryTaxonomyDatabase.pl [-version] -species "species name"
                                      [-isa "species name"]
                                      [-taxDBFile <RepeatMasker Taxonomy Database File>]

  A utility script to query the RepeatMasker Taxonomy database.
  See Taxonomy.pm for details on the database build process.
  

They are useful for seeing which species are in Repbase and their higher order tax, they are in the util directory

---

Using fungi That should gather together all repeats from all fungal genomes in RepBase into the search space.

[nut_B]

Thank you so much Medhat,

And so sorry to ask a bit tricky question. Actually i'm not sure that i understood its correct, or not? That you mean I should construct my own database first by using queryRepeatDatabase.pl or queryTaxonomyDatabase.pl, right? Or I can use the fungi as a species parameter ( ./RepeatMasker -species fungi filename.fasta ) And In my util directory have only : buildRMLibFromEMBL.pl, buildSummary.pl, calcDivergenceFromLign.pl, createRepeatLandscape.pl, dupliconToSVG.pl, getRepeatMaskerBatch.pl, queryRepeatDatabase.pl, queryTaxonomyDatabase.pl, rmOut2Fasta.pl, rmOutToGFF3.pl, rmToUCSTables.pl, trfMask, and wublastToCrossmatch.pl. This directory don't have RepBase, can you suggest me, please.

[Medhat]

You missed what I said

If i want to know the list of species in these tool and choose species

You can use this tools queryRepeatDatabase.pl and queryTaxonomyDatabase.pl as I told you this will give you information regarding your question

and by using fungi as I declared in my answer this will gather together all repeats from all fungal genomes in RepBase into the search space (you need not to construct any thing)

also you shall put this as a comment to my answer not as a new answer

[qwzhang0601]

Hi Medhat: How can I check which rodent species are in the rodent repeat library. I know we can select mouse and rat for "-species", I want to see whether there are other rodent species (e.g., naked mole rat, guinea pig).

Thanks

[Medhat]

you can use perl queryTaxonomyDatabase.pl -species "guinea"

It will give you:

RepeatMasker Taxonomy Database Utility
======================================
Species guinea is not in the database. Here is a list of possible similar
sounding substitutes:
  geina
  goumi
  ginaia
  guynia
  gamia
  gonia
  gauna
  goniaea
  gouinia
  gwenia

other way is to search this file repeatmasker/RepeatMasker/Libraries/taxonomy.dat

Answer 2

[Bioinfotec]

From 4.1.1 version, The utilities 'queryTaxonomyDatabase.pl' and 'queryRepeatDatabase.pl' are no longer included, since that data is now included in FamDB. The 'famdb.py' tool can be used to make many of the same queries as the removed utilies, and even more.

You can use it like this :

python famdb.py -i ./Librarys/dfam names <species>

See more information in https://github.com/Dfam-consortium/FamDB