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LOCARNA...AND-PLOT(1) User Contributed Perl DocumentationLOCARNA...AND-PLOT(1)

NAME
       locarnap-predict-and-plot.pl

SYNOPSIS
       locarnap-predict-and-plot.pl [options] [<annotation-file>]

DESCRIPTION
       Performs	boundary and reliability prediction and	draws all reliability
       plots according to annotation (given as file or read from standard
       input). The script is usually used after	generating alignments with
       locarnap-realign-all.pl as third	step in	a pipeline for refining	RNAz
       hits with LocARNA-P.

OPTIONS
       --help
	   Brief help message

       --man
	   Full	documentation

       --test
	   Test

       --output-dir=d
	   Output directory (def=Relplots)

       --dont-plot
	   Skip	plotting, only output

       --show-sw
	   Show	the structure weight in	the plot

       --revcompl
	   Draw	for reverse complement (3'-5')

       --write-subseq
	   Write the subsequence of fit

       --output-format=f
	   Output format (f = pdf or png, def=pdf)

       By default plots	are written to directory Relplots. The predictions are
       written to standard out as a table. A line of the table contains	of the
       locus  name,  start,end,	 and  orientation  of the RNAz prediction, the
       LocARNA prediction and the first	annotation, the	on and	off  value  of
       the fit,	and the	background and hit reliability.

perl v5.32.1			  2022-11-19		 LOCARNA...AND-PLOT(1)

Want to link to this manual page? Use this URL:
<https://man.freebsd.org/cgi/man.cgi?query=locarnap-predict-and-plot.pl&sektion=1&manpath=FreeBSD+Ports+15.0>

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