repeat_now
Sends DNA to the RepeatMasker email server for masking. Masked DNA and repeat info is returned via email.
The command line options used are those of the RepeatMasker2 email server:
Repeat options:
Default settings are for masking all type of repeats in a primate sequence.
-l(ow) does not mask low_complexity DNA or simple repeats
-int does not mask interspersed repeats (mask low complex/simple repeat only)
-m(us) masks rodent specific and mammalian wide repeats
-rod same as -mus
-mam masks repeats found in non-primate, non-rodent mammals
-cow same as -mam
-alu masks Alus (and 7SLRNA, SVA and LTR5) only (only for primate DNA)
-div {number] mask only those repeats that are less than number% diverged from the consensus sequence
-lib {filename] allows usage of a custom library (e.g. from another species)
-cutoff [number] sets cutoff score for masking repeats when using -lib (default 200, cutoff score of 250 guarantees no false positives)
running options
-q quick search; 5-10% less sensitive, but 3-4 times faster than default
-s slow search; 0-5% more sensitive, but 2.5 times slower than default
-mrna recommended when query is mRNA; sets GC level to 43% and skips a LINE1 search
-gc [number] use matrices calculated for 'number' percentage background GC level
-gccalc forces RepeatMasker to calculate the GC content even for sequences < 2 kb
-frag [number] maximum sequence length masked without fragmenting (default 101000)
-nocut skips the steps in which repeats are excised
-noisy prints cross_match progress report to screen (defaults to .stderr file)
Output options:
-a shows the alignments in a .align output file
-inv alignments are presented in the orientation of the repeat (with option -a)
-cut saves a sequence (in file.cut) from which young/full-length repeats are excised
-small returns complete .masked sequence in lower case
-xsmall returns repetitive regions in lowercase (rest capitals) rather than masked
-x returns repetitive regions masked with Xs rather than Ns
-poly reports simple repeats that may be polymorphic (in file.poly)
-ace creates an additional output file in ACeDB format
-u creates an untouched annotation file besides the manipulated file
-xm creates an additional output file in cross_match format (for parsing)
-flex creates an annotation file in which the widths of the columns is adjusted to the longest word in the column
Examples:
repeat_now Dna.seq Mask using defaults (for primate sequence).
repeat_now -m -s -a -u -xm Dna.seq Mask rodent repeats, provide extended output.
Last modified 4/20/99
Written by Jim Lund in the lab of Roger Reeves, Johns Hopkins University