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RNASNOOP(1)			 User Commands			   RNASNOOP(1)

NAME
       RNAsnoop	- manual page for RNAsnoop 2.4.14

SYNOPSIS
       RNAsnoop	[options]

DESCRIPTION
       RNAsnoop	2.4.14

       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  sec-
       ondary  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 spe-
       cial case of H/ACA snoRNA.  For	general	 purpose  target  predictions,
       please have a look at RNAduplex,	RNAup, RNAcofold and RNAplex. Accessi-
       bility effects can be estimated by RNAsnoop if a	RNAplfold  accessibil-
       ity 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 tar-
       get.

       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.

       --help Print help and exit

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

       -V, --version
	      Print version and	exit

   Input Options:
	      Below are	command	line options which alter the general input be-
	      havior of	RNAsnoop

       -L, --alignmentLength=INT
	      Limit the	extent of the interactions to L	nucleotides

	      (default=`25')

       -C, --constraint
	      Calculate	the stem structure subject to constraints.

	      (default=off)

	      The  program  reads  first the stem sequence, then a string con-
	      taining 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  un-
	      paired  in  spite	of constraints.	PF folding ignores constraints
	      of type "|".

       -s, --query=STRING
	      File containing the query	sequence.

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

       -t, --target=STRING
	      File containing the target sequence.

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

       -S, --suffix=STRING
	      Specificy	the suffix that	was added by RNAup to the  accessibil-
	      ity files

	      (default=`_u1_to_30.out')

       -P, --from-RNAplfold=STRING
	      Specify  the  directory where accessibility profile generated by
	      RNAplfold	are found

   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  -2.8(kcal/mol)  should  be given as
	      -280(decacal/mol)

       -A, --alignment-mode
	      Specify if RNAsnoop gets alignments or single sequences as input

	      (default=off)

       -f, --fast-folding=INT
	      Speedup of the target search  (default=`1')

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

       -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 interior	loops.
	      Only useful when no accessibility	profiles are  available.  This
	      option  is  disabled  if accessibility profiles are used (-P op-
	      tion)

       -o, --minimal-right-duplex=INT
	      Minimal Right Duplex Energy

	      (default=`-270')

       -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 -2.8
	      kcal/mol corresponds to -280 decacal/mol

       -p, --minimal-left-duplex=INT Minimal Left Duplex Energy

	      (default=`-170')

       -q, --minimal-duplex=INT
	      Minimal Duplex Energy

	      (default=`-1090')

       -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

       -h, --minimal-stem-length=INT Minimal snoRNA stem length

	      (default=`5')

       -i, --maximal-stem-length=INT Maximal snoRNA stem length

	      (default=`120')

       -j, --minimal-duplex-box-length=INT
	      Minimal distance between the duplex end and the

	      H/ACA box

	      (default=`11')

       -k, --maximal-duplex-box-length=INT
	      Maximal distance between the duplex end and the

	      H/ACA box

	      (default=`16')

       -m, --minimal-snoRNA-stem-loop-length=INT
	      Minimal number of	nucleotides between the

       beginning of stem loop and
	      beginning	of the snoRNA sequence

	      (default=`1')

       -n, --maximal-snoRNA-stem-loop-length=INT
	      Maximal number of	nucleotides between the

       beginning of stem loop and
	      beginning	of the snoRNA sequence

	      (default=`100000')

       -v, --minimal-snoRNA-duplex-length=INT
	      Minimal distance between duplex start and

	      snoRNA

	      (default=`0')

       -w, --maximal-snoRNA-duplex-length=INT
	      Maximal distance between duplex start and

	      snoRNA

	      (default=`0')

       -x, --minimal-duplex-stem-energy=INT
	      Minimal duplex stem energy

	      (default=`-1370')

       -y, --minimal-total-energy=INT
	      Minimal total energy

	      (default=`100000')

       -a, --maximal-stem-asymmetry=INT
	      Maximal snoRNA stem asymmetry

	      (default=`30')

       -b, --minimal-lower-stem-energy=INT
	      Minimal lower stem energy

	      (default=`100000')

   Output options:
	      Options that modifies the	output

       -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 -a is set	 or  the  energy  cor-
	      rected by	-c. If unset, only the mfe will	be returned

       -I, --produce-ps
	      Draw  annotated  2D  structures for a list of dot-bracket	struc-
	      tures

	      (default=off)

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

       -O, --output_directory=STRING Set where the generated figures should be
	      stored

	      (default=`./')

       -N, --direct-redraw
	      Outputs 2D interactions concurrently with	the interaction	calcu-
	      lation for each suboptimal interaction. The -I option should  be
	      preferred.

	      (default=off)

       -U, --from-RNAup=STRING
	      Specify  the directory where accessibility profiles generated by
	      RNAup are	found

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	Struc-
       tures", 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 al-
       gorithm 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.", Bioinfor-
       matics: 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 modifica-
       tion 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.

RNAsnoop 2.4.14			  August 2019			   RNASNOOP(1)

NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS

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