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EXTENDSTEM

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

extendstem - add/indicate possible stem extensions in RNA

 

SYNOPSIS

extendstem
[-c | --color | -Ccolor_r,color_g,color_b | --color=color_r,color_g,color_b] [-Dcolor_r,col-or_g,color_b | --color2=color_r,color_g,color_b] [-f | --fgcolor | -Fcolor_r,color_g,color_b | --fgcolor=color_r,color_g,color_b] [-Gcolor_r,col-or_g,color_b | --fgcolor2=color_r,color_g,color_b] [-g | --gupair] [-u | --toupper] [-ssupport | --support=support] [file]

 

DESCRIPTION

extendstem extends existing stems in RNA structures. Input is either from file or stdin. The output is sent to stdout.

extendstem can also be used to add/modify color columns to color nucleotides participating in possible stem extensions.

This program makes the obvious extensions of stem:


    AUGCAUGCUGCAA   to   AUGCAUGCUGCAA
    ...((...))...        .((((...)))).

Extensions are performed on CG and AU pairs. Loops will always have length 3. GU pairs are only made in situations where they are between AU, GC or known pairs:


    AUGUAUGCUGUAA   to   AUGUAUGCUGUAA
    ...((...))...        .((((...)))).


    AUGCAUGCUGUUA   to   AUGCAUGCUGUUA
    ...((...))...        ...((...))...

Anbiguous changes are not performed, e.g.:


    ...A((...))U((...))A...

 

OPTIONS

extendstem accepts the following options.

-c
--color
Color nucleotide background blue instead of changing the structure, and color ambigous extensions cyan.

-f
--fgcolor
Color nucleotide foreground blue instead of changing the structure, and color ambigous extensions cyan.

-Ccolor_r,color_g,color_b
--color=color_r,color_g,color_b
Like -c except that the rgb color of extension is specified. color_x are numbers between 0 and 1, setting the relevant color part.

-Dcolor_r,color_g,color_b
--color2=color_r,color_g,color_b
Specification of color for ambigous extensions, as above.

-Fcolor_r,color_g,color_b
--fgcolor=color_r,color_g,color_b
Like -f except that the rgb color of extension is specified. color_x are numbers between 0 and 1, setting the relevant color part.

-Gcolor_r,color_g,color_b
--fgcolor2=color_r,color_g,color_b
Specification of color for ambigous extensions, as above.

-g
--gupair
Let GU pairs have the same status as AU and GC.

-u
--toupper
Change stem extensions to upper case letters. Does not work with -c option.

-ssupport
--support=support
Only extend from supported base pairs, and only support positions away from them.

 

EXAMPLES

Extend stems in file foo.col:

extendstem foo.col

Color extensions blue and ambiguities cyan:

extendstem -c foo.col

Extend stems, with GU pairs treated as AU and GC pairs. Only extend to a distance of two to a supported pair. Also change the nucleotides in new pairs to upper case.

extendstem -g -s2 -u foo.col

 

BUGS

Ambigous extensions in some special pseudoknotted structures may be overlooked.

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