1.4 RNAdistance - calculate distances of RNA secondary structures Fontana, Hofacker, Stadler Shapiro B A, (1988) An algorithm for comparing multiple RNA secondary structures, CABIOS 4, 381-393 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 http://bioweb.pasteur.fr/docs/gensoft-na.html#VIENNARNA rnadistance rnadistance perl "RNAdistance" 0 struct Structures File perl " < $value" 1000 The program accepts structures in bracket format, where matching brackets symbolize base pairs and unpaired bases are represented by a dot '.', or coarse grained representations where hairpins, interior loops, bulges, multiloops, stacks and external bases are represented by (H), (I), (B), (M), (S), and (E), respectively. These can be optionally weighted. Full structures can be represented in the same fashion using the identifiers (U) and (P) for unpaired and paired bases, respectively. Examples: .((..(((...)))..((..)))). full structure (usual format); (U)((U2)((U3)P3)(U2)((U2)P2)P2) HIT structure; ((H)(H)M) or ((((H)S)((H)S)M)S) coarse grained structure; (((((H3)S3)((H2)S2)M4)S2)E2) weighted coarse grained. others_options Other options 2 distance Representation for distance calculation (-D) perl ($value && $value ne $vdef)? " -D$value" : "" f 2 f f: full (tree editing) F F: full (string alignment) h h: HIT (tree editing) H H: HIT (string alignment) w w: weighted coarse (tree editing) W W: weighted coarse (string alignment) c c: coarse (tree editing) C C: coarse (string alignment) P P: selects the base pair distance compare Which comparisons (-X) perl ($value && $value ne $vdef)? " -X$value" : "" p 2 p p: pairwise (1st/2nd, 3rd/4th etc) m m: distance matrix between all structures f f: each structure to the first one c c: continuously, that is i-th with (i+1)th structure matrix_options Analyse the distance matrix perl $compare eq "m" 2000 Only when comparison between all structures is requested (-Xm) This uses the beta test version of AnalyseDists distributed with the Vienna package. do_analyse Do this analysis (with AnalyseDists program) (-Xm only)? perl ($value)? " | AnalyseDists" : "" 0 2000 perl $compare eq "m" method Analysis methods to be used (-X) perl ($value && $value ne $vdef)? " -X$value" : "" s 2001 s s: split decomposition w w: cluster analysis using Ward's method n n: Cluster analysis using Saitou's neighbour joining method perl $compare eq "m" psfiles 2000 perl $compare eq "m" && $method eq "w" || $method eq "n" *.ps shapiro Use the Bruce Shapiro's cost matrix for comparing coarse structures (-S) perl ($value)? " -S" : "" 0 2 alignment_file Alignment file (-B) perl ($value)? " -B $value" : "" 2 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.