1. Unix system with RepeatMasker 3.2.0 or higher installed
   • DupMasker is included in the RepeatMasker 3.2.0 (and higher) release. RepeatMasker installation instructions can be found here
2. Sequence Search Engine
   DupMasker/RepeatMasker use a sequence search engine to perform their searches. Currently DupMasker only supports the RMBlast and WUBlast/ABBlast engines.
   • For RMBlast ( NCBI Blast modified for use with RepeatMasker/RepeatModeler ) please go to our download page: http://www.repeatmasker.org/rmblast
   • For ABBlast go to http://blast.advbiocomp.com/licensing/
3. Duplicon Database
   The duplicon database developed by Jiang Z. et al. is an essential component of this system. It is available for download from: dupliconlib-20080314.tar.gz

   Details on how this database was constructed may be found in:

   Jiang Z, Tang H, Ventura M, Cardone MF, Marques-Bonet T, She X, Pevzner PA, Eichler EE.
   "Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution."
   Nat Genet. 2007 Nov;39(11):1361-8. Epub 2007 Oct 7.

1. Install DupMasker Database
   Download the duplicon database and unpack it in the RepeatMasker program directory.
   • cp dupliconlib-20080314.tar.gz /usr/local/RepeatMasker
   • cd /usr/local/RepeatMasker
   • gunzip dupliconlib-20080314.tar.gz
   • tar xvf dupliconlib-20080314.tar
   • rm dupliconlib-20080314.tar

Forward Strand Annotation:

 SW    perc perc perc qry   qry   qry  qry   subj           subj  subj subj 
 score div. del. ins. seq   begin end (left) seq            begin end (left) 
 ---------------------------------------------------------------------------
 2334  8.44 0.00 3.25 chr1  127   737 (8222) SD1132...       1    298 (14)     

 SW    perc perc perc qry   qry   qry  qry     subj       subj  subj subj 
 score div. del. ins. seq   begin end (left) C seq       (left) end  begin  
 -------------------------------------------------------------------------
 2334  8.44 0.00 3.25 chr1  127   737 (8222) C SD1132...  (14)  298  1       

• SW score = smith-waterman score of the match (complexity-adjusted )
• perc div. = %substitutions in matching region.
• perc del. = %deletions (in query seq rel to subject) in matching region.
• perc ins. = %insertions (in query seq rel to subject) in matching region.
• qry seq = id of query sequence.
• qry begin = starting position of match in query sequence.
• qry end = ending position of match in query sequence.
• qry (left) = no. of bases in query sequence past the ending position of match (so 0 means that the match extended all the way to the end of the query sequence).
• C = "C" match is found on the reverse strand
• subj seq = id of the duplicon.
• subj (left) = The remaining bases in (complement of) subject sequence prior to beginning of the match.
• subj end = starting position of match in subject sequence (using top-strand numbering).
• subj begin = ending position of match in subject sequence.

• [DupMaskerPath]/DupMasker AC097264.4

• AC097264.4.dupout - An intermediate file of results obtained by searching the masked sequence against the duplicons library.
• AC097264.4.duplicons - The final output of fully-extended duplicons.

• [DupMaskerPath]/util/dupliconToSVG.pl AC097264.4.duplicons

• AC097264.4.duplicons.1.svg: Note: Some browsers can view this file directly. In addition firefox can zoom in and out on SVG files.

• A missing parameter to wublast in WUBlastSearchEngine.pm caused DupMasker to produce negative values in the *.duplicons file. This bug was only manifested when the input file contained NCBI accession identifiers such as "gi|238332|gb|AC839293.1|".
• Also in this release dupliconToSVG.pl was added to the RepeatMasker/util directory.

• Dupmasker now supports the GFF output format. Use the -gff option to generate a *.duplicons.gff file in addition to the *.duplicons file.
• A new utility has been written to convert the *.duplicons file ( ex hg18-chr1.duplicons ) into a Scalable Vector Graphics visualization of the duplication blocks ( ex hg18-chr1.duplicons.1.svg ). This utility is available as a separate download ( now in Repeatmasker package -- see above ). Run the program to view the documentation.

• First release of DupMasker.