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Info

Data Specification

Note: for informations about data importation, see " Algorithm Details " section ("Structure importation" subsection).

Structures Elements

RNA secondary structures represent paired bases in a plan. On this website, only Watson-Crick and Wobble pairs are considered as part of secondary structures. However, other kinds of pairing can be accepted. On the other hand, interactions between more than 2 bases are not allowed in secondary structures. Moreover, pseudoknots (including kissing loops/hairpins) are also not taken in account (except for the unaligning tool).

secondary structure elements

Caption
secondary structure elements sequence 5' end
secondary structure elements sequence 3' end
secondary structure elements strong Watson-Crick hydrogen bond (G-C and C-G)
secondary structure elements weak Watson-Crick hydrogen bond (A-U and U-A)
secondary structure elements Wobble hydrogen bond (G-U and U-G)
secondary structure elements stem-loop
secondary structure elements stem
secondary structure elements pairs stacking
secondary structure elements buldge
secondary structure elements internal loop
secondary structure elements hairpin loop
secondary structure elements multiple branch loop
secondary structure elements external base
secondary structure elements paired base
secondary structure elements buldge base
secondary structure elements internal loop base
secondary structure elements hairpin loop base
secondary structure elements multiple branch loop base

Supported structure data formats

At this time, this site handles 2 RNA secondary structure data format. The first one is the Fasta nucleotides sequences one with dotbracket annotation for pairings. The second one is the Connect or ".CT" format. In some cases, the user can also specify database structures by entering their ID in separate lines. In some other cases, it can be a format for structures alignment similar to the "Fasta dot-bracket format".
Note: for each of these data formats, only the 16 base codes described in "Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences" de l'IUPAC/IUB1 can be used ("T" is auto-converted into "U").
Note: so far, no XML data format is supported but developpments are made in that direction.

"Fasta Dot-Bracket" format

This format can contain 2 or 3 lines. The first one is optional and starts with the ">" character followed by the structure name. The second line contains the nucleotides sequence (from its 5' end to the 3' one). Finally, the third line contains the dot-bracket annotation of each sequence nucleotide: a dot tells the base is free and an opening bracket (actually a parenthesis) tells the base is paired with the base which is annotated by the corresponding closing bracket.

There are four major differences between dot-bracket Fasta format and traditional Fasta format. First, there's always a dot-bracket annotation line not present in the original Fasta format, following and having the same length of the nucleotides sequence line. Then, the sequence can be stored on one line of unlimited length while in the original Fasta format, the sequence can be stored on several lines of a maximum length of 80 charcters. Moreover, on this website, an additional character not included in the IUPAC/IUB is accepted in the sequence: the character "_". This one is used to indicates a nucleotide sequence split position to allow the use of stems (without haiprin loops) which are made of 2 disjoined sequence segments. To conclude, the first line containing the structure name can be omitted (the second line containing the sequence becomes the "first one").
Note: sometimes, 2 additional lines about pseudoknots are displayed. The first one contains "#>PSEUDOKNOTS" and the next one a dot-bracket annotation including pseudoknots where each upper case letter annotates a pseudoknot base paired with the base annotated by the corresponding lower case version of the same letter. So far, these lines are not handled by the large majority of tools here and should be removed.
Note: a derived verion of the dot-bracket Fasta format offering more flexibility, extendable and easier to parse and edit than XML format is currently being prepared.

Connect (.CT) format

The second supported format is the "Connect" format (or "CT"). The first line contains the structure nucleotides count, its folding free energy and its name. Each folling line describes a nucleotide on 6 columns (separated by spaces):

"Fasta dot-bracket" format for structures alignment

This format can contain one or more structure alignments records. Each record contains 2 structures in Fasta dot-bracket format with gap characters ("-") allowed in both the sequence and the dot-bracket annotation at the same positions. These 2 aligned structures are followed by 2 lines for the alignment scenario. The first line contains just the comment "#>SCENARIO". The next one contains the mutation event annotation for each position of the alignement:

m
m match a free base
s
s substitution of a free base
i
i insertion of a free base
d
d deletion of a free base
M
M match of a base pair (annotates each base of the pair)
H
H half-match of a base pair (annotates matched base of the pair)
h
h half-match of a base pair (annotates substituted base of the pair)
S
S substitution of a base pair (both bases in the pair are subtituted)
I
I insertion of a base pair
D
D deletion of a base pair
C
C completion of a base pair
c
c completion of a base pair with substitution
P
P creation of a base pair (pairing): the formation of an hydrogen bond between to existing free bases
p
p creation of a base pair (pairing) with substitution
A
A base pair altering
a
a base pair altering with substitution
B
B breaking of a base pair: deletion of the hydrogen bond between the two bases of a pair resulting in two free bases
b
b breaking of a base pair (annotated base was substituted)
R1
R rearranging one base of a base pair: the base in question bonds to another "partner"
r1
r rearranging one base of a base pair: the base in question is not bonded anymore
t
t insertion of a stem (tige) or stem-loop (annotated base is included in the inserted element)
T
T deletion of a stem (tige) or stem-loop (annotated base is included in the deleted element)
j
j connection (join) between two segments of a sequence
l
l split of a sequence into two segments
_
sequences split position matching (underscore character)
F2
folding of free bases (annotates the first base a the new pair)
f2
folding of free bases (annotates the second base a the new pair)
W1,3
change of side of a free base (side swap) (annotates the original position)
w1,3
change of side of a free base (side swap) (annotates the new position)