IntaRNA

IntaRNA

a program for the fast and accurate prediction of interactions between two RNA molecules

Sequence Parameters

Query ncRNA (short) in FASTA:

[clear]

... or, upload a file:

Target RNA (long) in FASTA:

[clear]

... or, upload a file:

[+] Output Parameters

Number of (sub)optimal interactions:

Suboptimal interaction overlap:

no overlap (in both)

can overlap in target

can overlap in query

can overlap in both

Max. absolute energy of an interaction:

Max. delta energy above mfe of an interaction:

[+] Seed Parameters

Min. number of basepairs in seed:

Max. Number of mismatches in seed:

Maximal energy:

Minimal unpaired probability (each):

Seed position (query):

Seed position (target):

[+] Folding Parameters

Temperature for energy computation:

Access. query: folding window size:

Access. query: max. basepair distance:

Access. target: folding window size:

Access. target: max. basepair distance:

Note

According to the rule of IntaRNA, thymine T encodings will be replaced by uracil U. If the position is N, not A/C/G/T/U, which will be not considered to form base pairs (and thus ignored).