dictionary of repeat names

[juan.a....@upc.edu]

Dear colleagues,
I am searching primate genomes for repeats found
in the RepeatMasker track. I have obtained several
tables but I am not sure if they are complete.
The problem is that the names which
are used do not correspond to those of the list
available in the giri website. For example in
order to search for alpha repeats I have to use
ALR/Alpha in the human case and ALRY_MAJOR_PT in
the chimpanzee. For pentanucleotides I do not
know which is the right name, for example (CAAAA)
could also be AACAA, TTTTG, etc.
I would like to have the name of all the repeats
used by you in each genome. I have not been able
to find it in your website, you send the user to
the list in giri...
Thank you for your help.
Cheers

Juan

Dr.Juan A. Subirana, Emeritus Professor, UPC TEL: 34-932093065
e-mail: Juan.A....@upc.edu
1) Department of Computer Science
Universitat Politècnica de Catalunya
2) Research Programme on Biomedical Informatics (GRIB)
Hospital del Mar Research Inst.(IMIM), Universitat Pompeu Fabra (UPF)
http://evolutionarygenomics.imim.es
Barcelona, Spain

[Matthew Speir]

Hi Juan,

Thank you for your question about the RepeatMasker track in the UCSC Genome Browser. It appears that you are confusing the "GIRI Repbase Reports library" with the "GIRI Repbase-derived RepeatMasker library". When using RepeatMasker to look for repeats in your species of interest, you should use the GIRI Repbase-derived RepeatMasker Library. In there, you will find the name, sequence and phylogenetic labels for each repeat so you can determine if that repeat is found in your organism of interest. One of the creators of RepeatMasker notes that if you download that library along with the RepeatMasker package, you can use one of the included utilities to find the repeats specific to an organism by running:

<RepeatMaskerDir>/util/queryRepeatDatabase.pl -species "human" -stat

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group