While VISTA automatically scans for repeat sequences, PipMaker does not incorporate this necessary step. Either you can first run VISTA and use its repeat report in PipMaker, or you can run RepeatMasker directly on your sequence. RepeatMasker scans for known repeats and returns a report of their positions. It is only necessary to mask the first sequence (the one that will be used as the base sequence).

Either browse for your sequence file or enter it into the query box. Select html as the return format and email as the return method. Enter your e-mail address. Choose the default speed/sensitivity method and the appropriate DNA source.

Hit the Submit Query button.

REPEATMASKER WEB SERVER

Current Version: 07/07/01

RepeatMasker screens DNA sequences in fasta format against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions.
Reference: A.F.A. Smit & P. Green, unpublished data.

Large sequences will be queued, and may take a while to process. Consider retrieving results by email, using the email server (send "help" to repeatmasker@ftp.genome.washington.edu) or running RepeatMasker locally (see below for contact)
Enter the file to process:

Or paste the sequence(s) in FASTA format:

Select return format: html tar file links
Select return method: html email

Speed/Sensitivity: quick default slow

DNA source:
Primates Rodents Other mammals Other vertebrates
Arabidopsis Grasses Drosophila

Options:
Show Alignments
Do not mask simple repeats and low complexity DNA
Only mask simple repeats and low complexity DNA
Only mask Alus
Mask with X's to distinguish masked regions from Ns already in query
Produce an annotation table with fixed width columns

Other options:

For faster service in Europe, try the mirror site at Germany.

RepeatMasker written and supported by Arian Smit.

Please send any requests or problem reports to the web site manager (webadmin at ftp.genome.washington.edu) .

The Genome Center home page