Database of repetitive sequences?

Bruce Roe broe at aardvark.ucs.uoknor.edu
Mon Mar 23 10:42:00 EST 1992


In article <9203210246.AA25358 at genbank.bio.net>, CLARK at SALK-SC2.SDSC.EDU writes...
>	I need a collection of human repetitive sequences that I will use 
>to prescreen sequences before we send them off for Fasta or Blast searches. 
>If anyone has or knows of a database of human repetitive sequences that I 
>could get, preferably by FTP, I would be most grateful to find out. I 
>checked in LIMB but only saw a reference to the Alu database. Even a list 
>of GenBank locus names or accession numbers would do.
>	Thanks in advance,
>Steve Clark
>clark at salk-sc2.sdsc.edu  (Internet)
>clark at salk               (Bitnet)
Steve,
	Since we are sequencing large regions (250 KB) in and
around the human cabl gene on chromsome9 and the bcr gene on
chromosome 22, I too have been curious about obtaining a data
base of repeated sequences.  Your question prompted me to look
deeper into the GCG documention and I came up with the following,
which by the way actually worked and now I've got a data set of
repeated sequences.  I'm really happy.  Thanks and give it a
try.

1. Run Strings:

	Search for the keyword "repeat" and search the GenEMBL
	database with the output set to GENEMBL.STRINGS

2. Run DataSet

	To create the GCG data library from the set of sequences
	in GCG format obtained as output from STRINGS

	Assemble DATASET from what sequence(s) ?  @genembl.strings

	What should I call the data library ?  repeats

3. Sit back and watch all the work get done for you.

Cheers...........bruce
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 \  Bruce A. Roe                     Dept. Chemistry and Biochemistry /
 /  BROE at aardvark.ucs.uoknor.edu     University of Oklahoma           \
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