mreps::howto

How to download it

at the address /mreps/mreps-2.5.tar.gz

How to install it

Issue the following commands:

  gunzip mreps.tar.gz
  tar -xvf mreps.tar
  cd mreps-2.5
  make

How to run it

The usage of mreps is

  mreps [ <options> ] { <sequencefile> | -s <sequence> }

Options

  -from n 	    process starting from position n
  -to n 	    process until position n
  -step n 	    process by sliding windows of size 2*n overlapping by n
 
  -minsize n 	    search for repetitions of size greater or equal to n
  -maxsize n 	    search for repetitions of size smaller or equal to n
  -minp n	    search for repetitions of period greater or equal to n
  -maxp n	    search for repetitions of period smaller or equal to n
  -exp x 	    search for repetitions of exponent greater or equal to x
 
  -res n            resolution parameter
 
  -allowsmall 	    switch off filtering out small repeats
 
  -xmloutput file   output to file in xml format
  -fasta 	    allow DNA sequences in fasta format (option used only with DNA version)
  -noprint 	    output only parameters of repetitions but not the sequences themselves
 
  -v, -vv, -vvv     verbose

Example

  > mreps -res -exp 3.0 -from 10000 -to 12000 -fasta ecolim52.fas

outputs all repeats of exponent >=3 computed with resolution 1 and occurring between positions 10000 and 12000 in the DNA sequence in fasta format stored in file ecolim52.fas