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).

Caption
sequence 5' end
sequence 3' end
strong Watson-Crick hydrogen bond (G-C and C-G)
weak Watson-Crick hydrogen bond (A-U and U-A)
Wobble hydrogen bond (G-U and U-G)
stem-loop
stem
pairs stacking
buldge
internal loop
hairpin loop
multiple branch loop
external base
paired base
buldge base
internal loop base
hairpin loop base
multiple branch loop baseSupported 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):
- 1st column: its number in the sequence;
- 2nd column: its base code;
- 3rd column: the number of the nucleotide connected on 5' (0 if none);
- 4th column: the number of the nucleotide connected on 3' (0 if none);
- 5th column: the number of the nucleotide paired with the current one;
- 6th column: once again, its number in the sequence.
"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
match a free base- s
substitution of a free base- i
insertion of a free base- d
deletion of a free base- M
match of a base pair (annotates each base of the pair)- H
half-match of a base pair (annotates matched base of the pair)- h
half-match of a base pair (annotates substituted base of the pair)- S
substitution of a base pair (both bases in the pair are subtituted)- I
insertion of a base pair- D
deletion of a base pair- C
completion of a base pair- c
completion of a base pair with substitution- P
creation of a base pair (pairing): the formation of an hydrogen bond between to existing free bases- p
creation of a base pair (pairing) with substitution- A
base pair altering- a
base pair altering with substitution- B
breaking of a base pair: deletion of the hydrogen bond between the two bases of a pair resulting in two free bases- b
breaking of a base pair (annotated base was substituted)- R1
rearranging one base of a base pair: the base in question bonds to another "partner"- r1
rearranging one base of a base pair: the base in question is not bonded anymore- t
insertion of a stem (tige) or stem-loop (annotated base is included in the inserted element)- T
deletion of a stem (tige) or stem-loop (annotated base is included in the deleted element)- j
connection (join) between two segments of a sequence- 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)
- Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res. 1985 May 10;13(9):3021-30.

RSS Feed