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RNASNOOP(1)			 User Commands			   RNASNOOP(1)

       RNAsnoop	- manual page for RNAsnoop 2.4.14

       RNAsnoop	[options]

       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-

       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

	      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


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


	      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


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

	      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

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


       -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-

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


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

	      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


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


       -d, --duplex-distance=INT
	      Distance between target 3' ends of two consecutive duplexes


	      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

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


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


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

	      H/ACA box


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

	      H/ACA box


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

       beginning of stem loop and
	      beginning	of the snoRNA sequence


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

       beginning of stem loop and
	      beginning	of the snoRNA sequence


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



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



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


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


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


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


   Output options:
	      Options that modifies the	output

       -e, --energy-threshold=DOUBLE Maximal energy difference between the mfe
	      the desired suboptimal


	      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-


	      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


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


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

       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

       Hakim Tafer, Ivo	L. Hofacker

       If  in doubt our	program	is right, nature is at fault.  Comments	should
       be sent to

RNAsnoop 2.4.14			  August 2019			   RNASNOOP(1)


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