RNAdistance accepts structures in bracket format, where matching
brackets symbolize base pairs and unpaired bases are represented by
a dot ".", or coarse grained representations where hairpins,
interior loops, bulges, multiloops, stacks and external bases are
represented by (H), (I), (B), (M), (S), and (E), respectively.
These can be optionally weighted. Full structures can be
represented in the same fashion using the identifiers (U) and (P)
for unpaired and paired bases, respectively. We call this the HIT
representation (you don't want to know what this means). For
example the following structure consists of 2 hairpins joined by a
multiloop:

.((..(((...)))..((..)))). full structure (usual format); (U)((U2)((U3)P3)(U2)((U2)P2)P2) HIT structure; ((H)(H)M) or ((((H)S)((H)S)M)S) coarse grained structure; (((((H3)S3)((H2)S2)M4)S2)E2) weighted coarse grained.

The program will continue to read new structures until a line consisting of the single character @ or an end of file condition is encountered. Input lines neither containing a valid structure nor starting with > are ignored.

- -D[fhwcFHWCP]
- use the full, HIT, weighted coarse, or coarse representation to
calculate the distance. Capital letters indicate string alignment
otherwise tree editing is used. Any combination of distances can be
specified.
**-DP**selects the base pair distance. The default if "f". - -Xp
- compare the structures pairwise (p), that is first with 2nd, third with 4th etc. This is the default.
- -Xm
- calculate the distance matrix between all structures. The output is formatted as a lower triangle matrix.
- -Xf
- compare each structure to the first one.
- -Xc
- compare continuously, that is i-th with (i+1)th structure.
- -S
- Use the Bruce Shapiro's cost matrix for comparing coarse structures.
- -B [file]
- Print an "alignment" with gaps of the structures, to show
matching substructures. The aligned structures are written to
*file*, if specified. Otherwise output is written to stdout, unless the -Xm option is set in which case "backtrack.file" is used.

Shapiro B A, Zhang K (1990) Comparing multiple RNA secondary structures using tree comparison, CABIOS 6, 309-318

Fontana W, Konings D A M, Stadler P F, Schuster P, (1993) Statistics of RNA secondary structures, Biopolymers 33, 1389-1404

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, 167-188

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Time: 07:19:16 GMT, February 23, 2011