From e47d4dbf50727507632a3fe1c755e3141252ead7 Mon Sep 17 00:00:00 2001
From: Daniel Barton
+ RNAalifold is part of the Vienna
+ RNA Secondary Structure Prediction and Comparison Package. It was
+ described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R.
+ Gruber, and Peter F. Stadler, RNAalifold: Improved consensus
+ structure prediction for RNA alignments. (BMC
+ Bioinformatics, 9:474, 2008).
+
+ Example RNAalifold Output
+ RNAalifold prints a consensus alignment and mfe structure to stdout with its
+ associated energy. Depending on the arguments given, other information such as
+ alternate structures are displayed below while base pairing probabilities (-p or --MEA
+ options) are stored in a separate 'alifold.out' file.
+
+
+G_UUUCAUU___AUGACGGCCUGUGCU_UAAA__CCUCC____GAG__C________GGGUCA_G_G_UCUGAU___CUUG_______GAGAC
+(.((((...........(((((((((........(((......)))............))))).).).))..................))))) (-19.16 = -11.80 + -7.36)
+(.((((...........(((((((((........(((......)))............))))).).).))..................))))) [-19.32]
+ frequency of mfe structure in ensemble 0.765639
+(.((((...........(((((((((........(((......)))............))))).).).))..................))))) -19.16 {-11.80 + -7.36}
+(.((((...........(((((((((........(((......)))............))))).).).))..................))))) { 13.20 MEA=92.14}
+
+Alifold.out
+ 6 89 9 99.2% 0.023 CG:29 GC:14 UA:9
+ 4 91 11 99.1% 0.028 CG:20 GC:11 UG:2 UA:17
+ 3 92 18 96.9% 0.090 CG:5 GC:2 GU:1 UG:4 AU:6 UA:25
+ 35 46 3 93.3% 0.195 CG:31 GC:16 UG:2 AU:5 UA:4
+ 36 45 10 93.6% 0.185 CG:16 GC:6 GU:1 UG:2 AU:8 UA:18
+ .
+ .
+ .
+
+ Running RNAalifold from Jalview
+ To run RNAalifold go to Webservices→RNA Structure Prediction
+ and choose RNAalifold Defaults to run with no arguments or
+ edit settings and run ... to adjust the parameters before running.
+ Details of all the RNAalifold parameters can be found in the
+ RNAalifold Manpage.
+ JABAWS and Jalview support a selection of the RNAalifold arguments only.
+
Supported Arguments which give alternate structures
+
+ Partition Function (-p)
+ Calculate the Partition Function and base pairing probability matrix in addition to the mfe
+ structure. A coarse representation of the pair probabilities in the from of a psuedo
+ bracket notation, as well as the centroid structure derived from the pair probabilities
+ are displayed. The most likely base pairings are stored in a separate file by RNAalifold
+ and represented in Jalview by a bar graph annotation line labelled 'Contact Probabilities'.
+
+ Maximum Expected Accuracy Structure (--MEA)
+ Calculate an MEA structure where the expected Accuracy is computed from the base pair
+ probabilities. A more detailed description is found in the
+ RNAfold documentation.
+
Example RNAalifold Structure Annotation rows
+ +
N4wUL_N)w9OhWTYC+dNA7>Qr!S?5)+UjXE
z68~#KI+xeTnpHPgjMJX+vwlxELvOiwXN CamiTYtzd^&!fZ? vjTsz8@*37L8xA@_nat&!U
z&J}z(H#hPE3YGT3A$w0 KD-uY&5edy&(@`3_WT~y4`1)=4_@S(=<#}~9#f*pQn( i0}|(p^g_
z$M8=!@}mXFhchynK1|Q-%Ef?PnC}yVQU7A`O}NGjE8H3BAPw3~W$j@?pE1y%h}=
z)eCq>sR(|Ev;_PD)t%@rJ}pj+!`f=c$u}t4B*o@e
z@-KzOEE+nQ&Y@#2CRgC3KI7qAh$SG5o5WMrw!PpHYRl6rd)L?O{
zi`Cvdd
z@~q3r3i0X)e$iQWXOgd?oU7j8E=d={zVL`u
zgs;)m*w{Fn>3_Z=1R8-QxYo4%$%#gr;DY<(&7Monb(^inm86_bB;??vaFcb%(e&Ic
zVF|2K>w3Npc}N?*ZJ5qtKa2e&+akqHbtCKRinX!_Vi1hd&7NpH(WWsT=Tt+0hc^!XY@F4J1IIRr#QV*7I^&Z`Y