Input Options:

Below are command line options which alter the general input behavior 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 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 "|".

-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 accessibility 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 recomputed 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 option)

-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 corrected by -c. If unset, only the mfe will be returned

-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

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

stored

(default=`./')

-N, --direct-redraw

Outputs 2D interactions concurrently with the interaction calculation 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