Can I use RepeatMasker for Fungi? If yes what are the options?
Also, is there is any other tool for prediction of LINE, SINE, ALU, Transposons?
Outside of its supplied database files, RepeatMasker can work with any FASTA file, so you can use it to mask anything.
In any case, RepBase does have elements from fungi, so RM will be able to do it by default. I couldn't comment on how complete the list of identified elements is for fungi, though. Use repeatmasker -help for the manual pages.
Some stats on the masked elements:
$ repeatmasker-4.0.6/util/queryRepeatDatabase.pl -species Fungi -stat | grep -v "^>"
queryRepeatDatabase
===================
RepeatMasker Database: RepeatMaskerLib.embl
Version: 20150807
Species: Fungi ( fungi )
174 ancestral and ubiquitous sequence(s) with a total length of 45804 bp
2 fungi specific repeats with a total length of 5596 bp
2268 lineage specific sequence(s) with a total length of 7073597 bp
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version 2.3.6
Ηi George, I am querying the latest RepeatMaskerLib.embl (24) and I find 0 fungi-specific and lineage-specific repeats,and only 2 ancestral . Is there any chance you have -and can share- older versions of the RepeatMasker Database such as the one you show here has 174 ancestral, 2 fungi-specific and 2268 lineage specific sequences? It seems that since repeatmasker went commercial, the content has changed alot! Many thanks, Romanos