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Distance table

Secondary Structures (max: 200)

From a file:
or in plain text:

↑ Load an example.

+ Select structures from database (popup)

Parameters

>Score Scheme Costs of operations are reals (signed floats).
For distances computation, the algorithm is looking for operations of minimal costs. In order to make sens, it is recommanded to use a null cost for matchings and a positive or null cost for other operations.
For scores computation, the algorithm is looking for operations maximizing the score. In order to make sens, it is recommanded to use high positive costs for matchings and negative or null costs for other operations.

Score scheme edit mode
edit using operations types
edit using involved bases
edit in expert mode

|| Nucleic chain splitting (ie. alignment of a stem-loop with a stem)
-- Joining the 3' end of nucleic chain and the 5' end of another one (ie. alignment of a stem with a stem-loop)

Single Base Mutation Pair Mutations Other Mutations
m Match M Full-Match A Alteration
r Substitution R Substitution C Completion
i Insertion I Insertion B Pair-Breaking
d Deletion D Deletion P Pair-Creation
      h Half-Match R Base rearranging

↑ Reset to default score scheme

  - -A A- -U U- -G G- -C C- AU UA GC CG GU UG pc Highlight edit operation of type:
-    
-A
A-
-U
U-
-G
G-
-C
C-
AU
UA
GC
CG
GU
UG
pb    

pc: pairs creation
pb: pairs breaking

↑ Reset to default score scheme

↑ Mirror upper right triangle on lower left triangle

↑ Mirror lower left triangle on upper right triangle

> Export score scheme in text format (for copy/paste onlyWarning: If you use the popup menu "Save as...", the document saved wont be the one of the popup but rather the one of the comparison form!)

> Import text format score scheme


Specify a cost:
Allowed base codes are (CBN, IUPAC-IUB):
A:AdenineR:Purine (A or G)B:Non-adenine (B follows A)
U:UracilY:Pyrimidine (C or U)V:Non-uracil (V follows U)
G:GuanineM:Amino (A or C)H:Non-guanine (H follows G)
C:CytosineK:Keto (G or U)D:Non-cytosine (D follows C)
N:aNy baseS:Strong hydrogen bonds
(G or C)
W:Weak hydrogen bonds
(A or U)

To specify a base-pair, just enter its two letters.
Note: order of bases in a pair is important (ie. "AU" is different from "UA").
edit into costs
break pair costs
create pair costs
rearranging paired base costs

Specified costs:This list contains edit costs you specified. Unspecified edit cost are automatically computed using the default score scheme. To know the default cost of an edit operation, juste use one of the 3 previous lines to enter the bases involved and the default score will be displayed automatically in the end of the line.

none

↑ Reset custom scores

Note: computation results are stored for only 168 hours.