DupMasker specifications


Unique identifier OMICS_25373
Name DupMasker
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A DNA sequence.
Input format FASTA
Output data Some information of all seed alignments and information of all chained duplicons with ancestral state information.
Output format TXT
Operating system Unix/Linux
License Open Source License v2.1
Computer skills Advanced
Stability Stable
Maintained Yes


Add your version


  • person_outline Evan Eichler <>

Additional information

Users need to install the DupMasker database and its parent tool, RepeatMasker.

Publications for DupMasker

DupMasker in publications

PMCID: 5123046
PMID: 27882922
DOI: 10.1038/ncomms13637

[…] purpose, we only used homology-based search for refseq (ref. ) human protein-coding genes and repetitive elements. the homology-based segmental duplicated region search was conducted using dupmasker programme. to calculate grch38 genome recovery rates of human assemblies, we conducted whole-genome alignments between each assembly (koref_s final contigs, koref_s final scaffolds […]

PMCID: 3038909
PMID: 21261979
DOI: 10.1186/1471-2148-11-23

[…] region in chr2, figure ), and to display such dna sequence similarity information graphically. the order and orientation of mosaic duplicons within complex duplication blocks was delineated with dupmasker [] with customized perl scripts., interphase nuclei were prepared from lymphoblast cell lines from human and three primate outgroup species as follows: human cell line gm12004 (coriell cell […]

PMCID: 2930074
PMID: 20729854
DOI: 10.1038/ng.643

[…] and completely sequenced the insert of each clone. we aligned the sequence to the human genome and to the s1 haplotype that we reconstructed with miropeats . final annotation with common repeats and dupmasker output describing the composition of segmental duplications was also included with customized perl scripts., we thank p. sudmant for useful discussions, g.m. cooper and t. brown […]

To access a full list of publications, you will need to upgrade to our premium service.

DupMasker institution(s)
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Institute for Systems Biology, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
DupMasker funding source(s)
Supported by an NIH grant GM058815 and a Rosetta Inpharmatics fellowship (Merck Laboratories).

DupMasker reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review DupMasker