RepeatMasker 07262001 screens DNA sequences for low complexity DNA sequences and interspersed repeats Smit. A, Green. P We still haven't published a paper on RepeatMasker yet but would appreciate it if you could refer to the web page (Smit,AFA and Green,P RepeatMasker at http://repeatmasker.genome.washington.edu/cgi-bin/RM2_req.pl) or otherwise to Smit, AFA and Green, P., unpublished results. nucleic:motifs nucleic:repeats motifs RepeatMasker RepeatMasker perl RepeatMasker 0 seq Sequence File perl " $value" 2 8 resfiles *.stderr *.tbl *.log *.cat *.out maskedseq "$seq.masked" seqfile perl 1 gff_file perl $gff *.gff species Species options 1 mus Masks rodent specific and mammalian wide repeats (-mus) perl ($value)? " -mus" : "" 0 1 mam Masks repeats found in non-primate, non-rodent mammals (-mammal) perl ($value)? " -mammal" : "" 0 1 ara Masks repeats found in Arabidopsis thaliana (-arabidopsis) perl ($value)? " -arabidopsis" : "" 0 1 droso Masks repeats found in Drosophilas (-drosophila) perl ($value)? " -drosophila" : "" 0 1 elegans masks repeats found in C. elegans (-elegans) perl ($value) ? " -elegans" : "" 0 1 lib Custom library (e.g. from another species) (-lib) perl ($value) ? " -lib $value":"" 1 is_only only clips E coli insertion elements (-is_only) perl ($value) ? " -is_only" : "" 0 1 is_clip clips IS elements before analysis (-is_clip) perl ($value) ? " -is_clip" : "" 0 1 no_is skips bacterial insertion element check (-no_is) perl ($value) ? " -no_is" : "" 0 1 rodspec only checks for rodent specific repeats (-rodspec) perl ($value) ? " -rodspec" : "" 0 1 primspec only checks for primate specific repeats (-primspec) perl ($value) ? " -primspec" : "" 0 1 masking_options Masking options 1 nolow Does not mask low_complexity DNA or simple repeats (-nolow) perl ($value)? " -nolow":"" 0 1 noint Only masks low complex/simple repeats (no interspersed repeats) (-noint) perl ($value)? " -noint":"" 0 1 alu Only masks Alus (and 7SLRNA, SVA and LTR5)(only for primate DNA) (-alu) perl ($value)? " -alu":"" 0 1 div Masks only those repeats that are less than this percent diverged from the consensus sequence (-div) perl (defined $value)? " -div $value" : "" 1 cutoff Sets cutoff score for masking repeats when using -lib (-cutoff) perl (defined $value && $value != $vdef)? " -cutoff $value" : "" 225 1 perl $lib running_options Running options 1 speed Program search speed -q -qq -s perl ($value) ? " $value" : "" Quick search: 5-10% less sensitive, 3-4 times faster than default. Rush job: about 10% less sensitive. Slow search: 0-5% more sensitive, 2.5 times slower than default. wublast use WU-blast, rather than cross_match as engine (-w) perl ($value) ? " -w" : "" gc Use matrices calculated for this percentage background GC level (-gc) perl (defined $value)? " -gc $value" : "" 1 gccalc Program calculates the GC content even for batch files/small seqs (-gccalc) perl ($value)? " -gccalc":"" 0 1 frag Maximum sequence length masked without fragmenting (-frag) perl (defined $value && $value != $vdef)? " -frag $value" : "" 51000 1 nocut Skips the steps in which repeats are excised (-nocut) perl ($value)? " -nocut":"" 0 1 noisy Prints cross_match progress report to screen (-noisy) perl ($value) ? " -noisy ": "" 0 1 output_options Output options 1 align Shows the alignments in a .align output file (-a) perl ($value) ? " -a" : "" 0 1 inv Alignments are presented in the orientation of the repeat (with option -a) (-inv) perl ($value)? " -inv":"" 0 1 perl $a cut Saves a sequence (in file.cut) from which full-length repeats are excised (-cut) perl ($value)? " -cut":"" 0 1 small Returns complete masked sequence in lower case (-small) perl ($value)? " -small":"" 0 1 xsmall Returns repetitive regions in lowercase (rest capitals) rather than masked (-xsmall) perl ($value)? " -xsmall":"" 0 1 maskx Returns repetitive regions masked with Xs rather than Ns (-x) perl ($value)? " -x":"" 0 1 poly Reports simple repeats that may be polymorphic (in file.poly) (-poly) perl ($value)? " -poly":"" 0 1 ace Creates an additional output file in ACeDB format (-ace) perl ($value)? " -ace":"" 0 1 gff Creates a General Feature Finding format output (-gff) perl ($value)? " -gff":"" 0 1 u Creates an untouched annotation file besides the manipulated file (-u) perl ($value)? " -u":"" 0 1 xm Creates an additional output file in cross_match format (for parsing) (-xm) perl ($value)? " -xm":"" 0 1 fixed Creates an (old style) annotation file with fixed width column (-fixed) perl ($value)? " -fixed":"" 0 1 no_id leaves out final column with unique ID for each element (-no_id) perl ($value) ? " -no_id" : "" 0 1 excln calculates repeat densities excluding runs of >25 Ns in query (-e) perl ($value) ? " -e" : "" 0 1 aligfile perl $align *.align cutfile perl $cut *.cut polyfile perl $poly *.poly* acefile perl $ace *.ace gbfile perl $gbannot *.gb