Search stems / stem-loops

Query stem/stem-loop

From a file:
or in plain text:

↑ Load an example.

Advanced parameters

Match structural elements of same nature
Match with stems only
Match with stem-loops only
Match with either stems or stem-loops

Algorithm:Technical details about algorithms can be found on the page "Info>Algorithms Details".

Alignment computation type
by edit distanceComputes the minimal cost to transform a structure into another one.
by global scoreComputes the maximal correspondence score between two structures.

backtrack structures alignmentIf you check this option, alignment algorithm will add to the computed score the structures alignment which is the mapping between bases or hydrogen bonds of compared structures. This requiers more memory and time than just computing a score and you are encouraged to uncheck this option if you do not need structural alignments.
algorithmic details in raw outputIf you check this option the alignment algorithm will output details like the distance matrix and some backtracking info. You can download these outputs using the "Download raw output" link on result page.

>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:

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.


↑ Reset custom scores