IntaRNA

IntaRNA 2.0, a program for the fast and accurate prediction of interactions between two RNA molecules. For detailed information, please refer to IntaRNA.

Martin Mann, Patrick R. Wright, and Rolf Backofen. IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions Nucleic Acids Res., 2017, 45 (W1), W435–W439.

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:

Contact wangdong79@smu.edu.cn