########
RNAsnoop
########

:program:`RNAsnoop` - manual page for RNAsnoop 2.7.2

Synopsis
--------

.. code:: bash

    RNAsnoop [options]

DESCRIPTION
-----------

RNAsnoop 2.7.2

Find targets of a query H/ACA snoRNA

reads a target RNA sequence and a H/ACA snoRNA sequence
from a target and query file, respectively and computes optimal
and suboptimal secondary structures for their hybridization. The
calculation can be done roughly in O(nm), where is n the length
of the target sequence and m is the length of the snoRNA stem, as it
is specially tailored to the special case of H/ACA snoRNA. For general
purpose target predictions, please have a look at RNAduplex, RNAup,
RNAcofold and RNAplex. Accessibility effects can be estimated by
RNAsnoop if a RNAplfold accessibility profile is provided.

The computed optimal and suboptimal structure are written to
stdout, one structure per line. Each line consist
of: The structure in dot bracket format with a ``&`` separating the
two strands. The ``<>`` brackets represent snoRNA intramolecular
interactions, while the ``()`` brackets represent intermolecular
interactions between the snoRNA and its target.

The range of the structure in the two sequences in the format
"from,to : from,to"; the energy of duplex structure in
kcal/mol. If available the opening energy are also returned.

.. option:: --help

    Print help and exit

.. option:: --detailed-help

    Print help, including all details and hidden options, and exit

.. option:: --full-help

    Print help, including hidden options, and exit

.. option:: -V, --version

    Print version and exit

.. option:: --verbose

    Be verbose. *(default=off)*


    Lower the log level setting such that even INFO messages are passed through.

I/O Options:
^^^^^^^^^^^^



    Command line options for input and output (pre-)processing

.. option:: -s, --query=STRING

    File containing the query sequence.


    Input sequences can be given piped to RNAsnoop or given in a query file with
    the :option:`-s` option. Note that the :option:`-s` option implies that the :option:`-t` option is also
    used.

.. option:: -t, --target=STRING

    File containing the target sequence.


    Input sequences can be given piped to RNAsnoop or given in a target file with
    the :option:`-t` optionNote that the :option:`-t` option implies that the :option:`-s` option is also used.

.. option:: -S, --suffix=STRING

    Specificy the suffix that was added by RNAup to the accessibility files.


    *(default="_u1_to_30.out")*

.. option:: -P, --from-RNAplfold=STRING

    Specify the directory where accessibility profile generated by RNAplfold are found.

.. option:: -U, --from-RNAup=STRING

    Specify the directory where accessibility profiles generated by RNAup are found.

.. option:: -O, --output_directory=STRING Set where the generated figures should be

    stored.


    *(default="./")*

.. option:: --log-level=level

    Set log level threshold. *(default="2")*


    By default, any log messages are filtered such that only warnings (level 2)
    or errors (level 3) are printed. This setting allows for specifying the log
    level threshold, where higher values result in fewer information. Log-level 5
    turns off all messages, even errors and other critical information.

.. option:: --log-file[=filename]

    Print log messages to a file instead of stderr. *(default="RNAsnoop.log")*

.. option:: --log-time

    Include time stamp in log messages.


    *(default=off)*

.. option:: --log-call

    Include file and line of log calling function.


    *(default=off)*

Algorithms:
^^^^^^^^^^^



    Options which alter the computing behaviour of RNAplex. Please note that the
    options allowing to filter out snoRNA-RNA duplexes expect the energy to be
    given in decacal/mol instead of kcal/mol. A threshold of :option:`-2`.8(kcal/mol)
    should be given as :option:`-280`(decacal/mol).

.. option:: -A, --alignment-mode

    Specify if RNAsnoop gets alignments or single sequences as input.


    *(default=off)*

.. option:: -f, --fast-folding=INT

    Speedup of the target search. *(default="1")*


    This option allows one to decide if the backtracking has to be
    done (:option:`-f` 1) or not (:option:`-f` 0). For :option:`-f` 1 the structure is computed based
    on the standard energy model. This is the slowest mode of RNAsnoop. :option:`-f`
    0 is the fastest mode, as no structure are recomputed and only the
    interaction energy is returned.

.. option:: -c, --extension-cost=INT

    Cost to add to each nucleotide in a duplex. *(default="0")*


    Cost of extending a duplex by one nucleotide. Allows one to find
    compact duplexes, having few/small bulges or internal loops. Only
    useful when no accessibility profiles are available. This option is
    disabled if accessibility profiles are used (:option:`-P` option).

.. option:: -e, --energy-threshold=DOUBLE Maximal energy difference between the mfe and

    the desired suboptimal.


    *(default="-1")*


    Energy range for a duplex to be returned. The threshold is set on the total
    energy of interaction, i.e. the hybridizationenergy corrected for opening
    energy if :option:`-a` is set or the energy corrected by :option:`-c`. If unset, only the mfe
    will be returned.

.. option:: -o, --minimal-right-duplex=INT

    Minimal Right Duplex Energy


    *(default="-270")*

.. option:: -l, --minimal-loop-energy=INT Minimal Right Duplex Energy.

    *(default="-280")*


    Minimal Stem Loop Energy of the snoRNA. The energy should be
    given in decacalories, i.e. a minimal stem-loop energy of :option:`-2`.8
    kcal/mol corresponds to :option:`-280` decacal/mol.
.HP
:option:`-p`, :option:`--minimal-left-duplex`=*INT* Minimal Left Duplex Energy.


    *(default="-170")*

.. option:: -q, --minimal-duplex=INT

    Minimal Duplex Energy.


    *(default="-1090")*

.. option:: -d, --duplex-distance=INT

    Distance between target 3' ends of two consecutive duplexes.


    *(default="2")*


    Distance between the target 3'ends of two consecutive
    duplexes. Should be set to the maximal length of interaction to get
    good results. Smaller d leads to larger overlaps between consecutive
    duplexes.
.HP
:option:`-h`, :option:`--minimal-stem-length`=*INT* Minimal snoRNA stem length.


    *(default="5")*
.HP
:option:`-i`, :option:`--maximal-stem-length`=*INT* Maximal snoRNA stem length.


    *(default="120")*

.. option:: -j, --minimal-duplex-box-length=INT

    Minimal distance between the duplex end and the


    H/ACA box.


    *(default="11")*

.. option:: -k, --maximal-duplex-box-length=INT

    Maximal distance between the duplex end and the


    H/ACA box.


    *(default="16")*

.. option:: -m, --minimal-snoRNA-stem-loop-length=INT

    Minimal number of nucleotides between the

.. option:: beginning of stem loop and

    beginning of the snoRNA sequence.


    *(default="1")*

.. option:: -n, --maximal-snoRNA-stem-loop-length=INT

    Maximal number of nucleotides between the

.. option:: beginning of stem loop and

    beginning of the snoRNA sequence.


    *(default="100000")*

.. option:: -v, --minimal-snoRNA-duplex-length=INT

    Minimal distance between duplex start and


    snoRNA.


    *(default="0")*

.. option:: -w, --maximal-snoRNA-duplex-length=INT

    Maximal distance between duplex start and


    snoRNA.


    *(default="0")*

.. option:: -x, --minimal-duplex-stem-energy=INT

    Minimal duplex stem energy.


    *(default="-1370")*

.. option:: -y, --minimal-total-energy=INT

    Minimal total energy.


    *(default="100000")*

.. option:: -a, --maximal-stem-asymmetry=INT

    Maximal snoRNA stem asymmetry.


    *(default="30")*

.. option:: -b, --minimal-lower-stem-energy=INT

    Minimal lower stem energy.


    *(default="100000")*

.. option:: -L, --alignmentLength=INT

    Limit the extent of the interactions to L nucleotides.


    *(default="25")*

Structure Constraints:
^^^^^^^^^^^^^^^^^^^^^^



    Command line options to interact with the structure constraints feature of
    this program

.. option:: -C, --constraint

    Calculate the stem structure subject to constraints.


    *(default=off)*


    The program reads first the stem sequence, then a string containing
    constraints on the structure encoded with the symbols:


    . (no constraint for this base)


    | (the corresponding base has to be paired


    x (the base is unpaired)


    < (base i is paired with a base j>i)


    > (base i is paired with a base j<i)


    and matching brackets ( ) (base i pairs base j)


    With the exception of "|", constraints will disallow all pairs conflicting
    with the constraint. This is usually sufficient to enforce the constraint,
    but occasionally a base may stay unpaired in spite of constraints. PF folding
    ignores constraints of type "|".

Plotting:
^^^^^^^^^



    Command line options for changing the default behavior of structure layout
    and pairing probability plots.

.. option:: -I, --produce-ps

    Draw annotated 2D structures for a list of dot-bracket structures.


    *(default=off)*


    This option allows one to produce interaction figures in PS-format with
    conservation/accessibility annotation, if available.

.. option:: -N, --direct-redraw

    Outputs 2D interactions concurrently with the interaction calculation for each suboptimal interaction. The :option:`-I` option should be preferred.


    *(default=off)*

REFERENCES
----------

*If you use this program in your work you might want to cite:*

R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011),
"ViennaRNA Package 2.0",
Algorithms for Molecular Biology: 6:26

I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994),
"Fast Folding and Comparison of RNA Secondary Structures",
Monatshefte f. Chemie: 125, pp 167-188

R. Lorenz, I.L. Hofacker, P.F. Stadler (2016),
"RNA folding with hard and soft constraints",
Algorithms for Molecular Biology 11:1 pp 1-13

The calculation of duplex structure is based on dynamic programming algorithm originally
developed by Rehmsmeier and in parallel by Hofacker.

H. Tafer, S. Kehr, J. Hertel, I.L. Hofacker, P.F. Stadler (2009),
"RNAsnoop: efficient target prediction for H/ACA snoRNAs.",
Bioinformatics: 26(5), pp 610-616

*The energy parameters are taken from:*

D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker, D.H. Turner (2004),
"Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure",
Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292

D.H Turner, D.H. Mathews (2009),
"NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure",
Nucleic Acids Research: 38, pp 280-282

AUTHOR
------


Hakim Tafer, Ivo L. Hofacker

REPORTING BUGS
--------------


If in doubt our program is right, nature is at fault.
Comments should be sent to rna@tbi.univie.ac.at.