Repeatmasker

Category(ies): Bioinformatics

Version: 3.25(3.19,(3.16, 3.15 also available)

Author / Distributor: Author: A.F.A. Smit, R. Hubley & P. Green, Institute For Systems Biology

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program.

altix: Not available on altix

pcluster: Not available on pcluster

rcluster,IOB: running program | Documentation | Installation | System

Running Program: also refer to submit jobs to queues at rcluster,IOB

Cross_match and Wublast are configured as search engines.

RepeatMasker filename -e wublast

bsub -q queueName RepeatMasker filename -e wublast -o filename.out

* Current RepeatMasker library is RepBase13.06.embl.tar.gz
* version 3.19 avaialabel at /usr/local/RepeatMasker.3.19
* version 3.16 avaialabel at /usr/local/RepeatMasker.3.16
* version 3.15 avaialabel at /usr/local/RepeatMasker.3.15

Documentation: Online document available at RepeatMakser website

Installation: source downloaded from RepeatMasker , library updated from Repbase.

System(s): Unix