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


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