Robert Hubley

RepeatMasker employs a search strategy that identified nested insertions in a sequence. In the case you displayed above it looks like an AluY inserted inside a pre-existing L1MA7 insertion. It...

Unfortunately we do not have a way to handle this at this time. There is a limited set of classes due to the limited set of colors allowed in the...

This looks like a configuration problem with the path to ABBlast. Did you run the configure program and setup ABBlast when you installed RepeatMasker?

I have avoided doing this because of dependency checking. The configure script takes care of performing perl module dependency checking prior to setting the interpreter at the top of each...

Hi, I moved your issue to the RepeatMasker git repository because RepeatProteinMask is part of that package and not RepeatModeler. RepeatProtein mask is a simple wrapper around blastp and our...

Hi @bhdobrin, let me see if I can help. There is quite a bit here so let me start from the top. In the current release of Dfam (3.7) we...

Could you give me a little more background on how you are using RepeatMasker? ie. repeatmasker version, search engine, library version ( Dfam/Repbase ), and finally the command line used....

Oh...that's probably a bug. If you edit the WUBlastSearchEngine.pm file in RepeatMasker (near line 286): ``` # BLASTN 3.0-SE [2009-05-25] [linux26-x64-I32LPF64 2009-05-25T22:58:29] if ( $result =~ /^(BLAST[PN]) (\S+ \[.*\])/m )...

This has been fixed in RepeatMasker 4.1.5 released today.

Sorry for the delay. Are you still having this problem? The issue appears to be with the installation of RepeatMasker. The function referenced in the error was introduced in RepeatMasker...