R-chie [ɑrči]
A web server and R package for plotting RNA secondary structures, trans RNA-RNA interactions and genomic interactions.
EXAMPLE LOADED: Click Plot to see webserver in action, or Reset to submit own input.

Secondary Structure Input

Paste a secondary structure in dot-bracket, connect, bpseq, helix, new helix, or new genome interaction file format.
(Click format names for example, hover on names for format details)

MISSING INPUT: Please paste of upload input data.

[clear]
OR Upload a file:
INVALID VALUE: Please input integer.
INVALID VALUE: Please input valid string.

Input Processing Options

INVALID VALUE: Please input valid number.
Sort basepairs by value in order  Help icon
Filter out basepairs with values: < and > Help icon

Appearance Options

OPTIONS IGNORED: Options ignored when plotting as reference.
INVALID VALUE: Please input valid number.
INVALID RULE: Rule requires multiple sequence alignment.
No. of Groups Colour Palette Grouping Rule
[reset]
 Help icon  Help icon  Help icon
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No Scale Help icon No Legend Help icon
Up arrowDown arrowHelp icon

Please select shape:



(Optional) Your e-mail for job completion notice:

Add another structure to plot

Plot structure as individual structure
 
Plot structure as a known reference

Secondary Structure Input

Paste a secondary structure in dot-bracket, connect, bpseq, helix, new helix, or new genome interaction file format.
(Click format names for example, hover on names for format details)

MISSING INPUT: Please paste of upload input data.

[clear]
OR Upload a file:
INVALID VALUE: Please input integer.
INVALID VALUE: Please input valid string.

Input Processing Options

INVALID VALUE: Please input valid number.
Sort basepairs by value in order  Help icon
Filter out basepairs with values: < and > Help icon

Appearance Options

OPTIONS IGNORED: Options ignored when plotting as reference.
INVALID VALUE: Please input valid number.
INVALID RULE: Rule requires multiple sequence alignment.
No. of Groups Colour Palette Grouping Rule
[reset]
 Help icon  Help icon  Help icon
1
2
3
4
5
6
7
8
No Legend Help icon
Up arrowDown arrowHelp icon

Please select shape:



(Optional) Your e-mail for job completion notice:

Add nucleotide sequence(s) to plot

Multiple Sequence Alignment

Paste a multiple sequence alignment of one or more sequences in FASTA or new FastaMltp format. (Click format names for example, hover on name for details)

MISSING INPUT: Please paste of upload input data.
[clear]
OR Upload a file:

Sequence Appearance Options

Sequence appearance:
Draw sequences as lines
Draw sequences as blocks
Text information (only with "block" sequences):
Display species name of sequence
Display sequence nucleotides as text
Colour sequence by :
No Legend
Conservation Covariation One-sided Invalid Pair Unpaired Gap Ambiguous
A U/T G C Gap Ambiguous
(Optional) Your e-mail for job completion notice:

Add Second nucleotide sequence(s) to plot

Multiple Sequence Alignment

Paste a multiple sequence alignment of one or more sequences in FASTA or new FastaMltp format. (Click format names for example, hover on name for details)

MISSING INPUT: Please paste of upload input data.
[clear]
OR Upload a file:

Sequence Appearance Options

Sequence appearance:
Draw sequences as lines
Draw sequences as blocks
Text information (only with "block" sequences):
Display species name of sequence
Display sequence nucleotides as text
Colour sequence by :
No Legend
Conservation Covariation One-sided Invalid Pair Unpaired Gap Ambiguous
A U/T G C Gap Ambiguous
(Optional) Your e-mail for job completion notice:
Questions, comments, or problems?
e-RNA.org | Meyer Lab | MDC Berlin
Last update on 19. December 2022.