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PILERCR(1) User Commands PILERCR(1)

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:

Sequence file to analyze (FASTA format).
Report file name (plain text).
Save consensus sequences to this FASTA file.
Eliminate similar seqs from -seq file.
Don't write help to report file.
Don't write progress messages to stderr.

Criteria for CRISPR detection, defaults in parentheses:

Must be at least <n> repeats in array (3).
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.
Minimum repeat length (16).
Maximum repeat length (64).
Minimum spacer length (8).
Maximum spacer length (64).
Minimum repeat ratio (0.9).
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:

Minimum alignment length (16).
Minimum identity (0.94).
August 2021 pilercr 1.06+dfsg