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SUPPORT

Section: User Commands (1)
Updated: September 2000
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NAME

support - check support for RNA structure.  

SYNOPSIS

support
[-s | --support] [-llimit | --limit=limit] [file]
 

DESCRIPTION

support checks a structural alignment for which of the annotated pairs are supported in the sense that a fraction of at least limit is one of the six standard pairs. The default value for limit is 2/3.

If support is used as a filter it reads the entire file to memory, which can be quite memory consuming. If file is present, memory consumption is minimal. The output is sent to stdout.

A support column is added, which has `S' if the pairs are supported, `N' if there is an inconsistency with the structural alignment, otherwise `.'. An inconsistent column is a column in which different sequences have different pairs.  

OPTIONS

support accepts the following options.

-llimit
--limit=limit
Sets the limit for support. The default is 2/3.

-s
--support
Support information is output as the last entry.
 

EXAMPLES

Find columns with 3/4 support

support -l0.75 foo.col

This version uses more memory

cat foo.col | support -l0.75
 

BUGS

Report bugs to col-bugs@bioinf.au.dk.  

AUTHOR

Bjarne Knudsen (bk@daimi.au.dk)  

SEE ALSO


 

Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
BUGS
AUTHOR
SEE ALSO


Comments, questions, etc., email gorodkin@genome.ku.dk.


Last updated March 26th, 2007 by Jan Gorodkin