NAME
pilercr - software for finding CRISPR repeats
DESCRIPTION
pilercr v1.06 http://www.drive5.com/piler
AUTHOR
Written by Robert C. Edgar This software is donated to the public domain. Please visit web site for requested citation.
Basic options:
- -in <filename>
-
Sequence file to analyze (FASTA format).
- -out <filename>
-
Report file name (plain text).
- -seq <filename>
-
Save consensus sequences to this FASTA file.
- -trimseqs
-
Eliminate similar seqs from -seq file.
- -noinfo
-
Don't write help to report file.
- -quiet
-
Don't write progress messages to stderr.
Criteria for CRISPR detection, defaults in parentheses:
- -minarray <N>
-
Must be at least <n> repeats in array (3).
- -mincons <F>
-
Minimum conservation (0.9). At least N repeats must have identity >= F with the consensus sequence. Value is in range 0 .. 1.0. It is recommended to use a value < 1.0 because using 1.0 may suppress true arrays due to boundary misidentification.
- -minrepeat <L>
-
Minimum repeat length (16).
- -maxrepeat <L>
-
Maximum repeat length (64).
- -minspacer <L>
-
Minimum spacer length (8).
- -maxspacer <L>
-
Maximum spacer length (64).
- -minrepeatratio <R>
-
Minimum repeat ratio (0.9).
- -minspacerratio <R>
-
Minimum spacer ratio (0.75). 'Ratios' are defined as minlength / maxlength, thus a value close to 1.0 requires lengths to be similar, 1.0 means identical lengths. Spacer lengths sometimes vary significantly, so the default ratio is smaller. As with -mincons, using 1.0 is not recommended.
Parameters for creating local alignments:
- -minhitlength <L>
-
Minimum alignment length (16).
- -minid <F>
-
Minimum identity (0.94).