[Genome] chromFa.zip file

[Ann Zweig]

Hello David,

	The chromFa.zip file contains the sequence masked by Repeat Masker and by TRF 
(only those simple repeats with a period of 12 or less). Non-repeating sequence 
is shown in upper case, whereas all of the following repeats are shown in lower 
case:

# Short interspersed nuclear elements (SINE), which include ALUs
# Long interspersed nuclear elements (LINE)
# Long terminal repeat elements (LTR), which include retroposons
# DNA repeat elements (DNA)
# Simple repeats (micro-satellites)
# Low complexity repeats
# Satellite repeats
# RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
# Other repeats, which includes class RC (Rolling Circle)
AND
# TRF simple repeats with a period of 12 or less


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



> Subject:
> chromFa.zip file
> From:
> David L Klinkebiel <dklinkebiel at unmc.edu>
> Date:
> Wed, 7 May 2008 15:46:51 -0500
> To:
> genome at soe.ucsc.edu
> 
> To:
> genome at soe.ucsc.edu
> 
> 
> Is the Tandem Repeats Finder described in the chromFa.zip file the same as that present in the Genome browser described as Simple Tandem Repeats by TRF?
> chromFa.zip - The assembly sequence in one file per chromosome.
>     Repeats from RepeatMasker and Tandem Repeats Finder (with period
>     of 12 or less) are shown in lower case; non-repeating sequence is
>     shown in upper case. Repeat masking was done using the following
>     RepeatMasker/RepBase versions: RepBase Update 9.11, RM database 
>     version 20050112. 
> Does the chromFa.zip contain masked
> 
>     * Short interspersed nuclear elements (SINE), which include ALUs
>     * Long interspersed nuclear elements (LINE)
>     * Long terminal repeat elements (LTR), which include retroposons
>     * DNA repeat elements (DNA)
>     * Simple repeats (micro-satellites)
>     * Low complexity repeats
>     * Satellite repeats
>     * RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
>     * Other repeats, which includes class RC (Rolling Circle)
>     * Unknown
>     *
> 
>     * Plus Simple Tandem Repeats by TRF
> 
> Thanks
> 
> David Klinkebiel, Ph.D.
> Department of Biochemistry and Molecular Biology
> University of Nebraska Medical Center
> 985870 Nebraska Medical Center
> Omaha, NE 68198-5870
> Office Phone: 402-559-3842
> Lab Phone: 402-559-9303
> FAX: 402-559-6650
> 
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