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Algorithm independent properties of RNA secondary structure predictions |
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| Authors: | Manfred Tacker Peter F Stadler Erich G Bornberg-Bauer Ivo L Hofacker P Schuster |
| Institution: | ?sterreichisches Verpackungsinstitut für Lebens- und Genu?mittel, Franz-Grill-Strasse 5, A-1030 Wien, Austria, AT Institut für Theoretische Chemie, Universit?t Wien, W?hringerstrasse 17, A-1090 Wien, Austria (Fax: +43 1 40480 660; e-mail: pkstbi.univie.ac.at), AT Abteilung für Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany, DE Beckman Institute, 495 N Mathews, Urbana, Il 61801, USA, US |
| Abstract: | Algorithms predicting RNA secondary structures based on different folding criteria – minimum free energies (mfe), kinetic folding (kin), maximum matching (mm) – and different parameter sets are studied systematically. Two base pairing alphabets were used: the binary GC and the natural four-letter AUGC alphabet. Computed structures and free energies depend strongly on both the algorithm and the parameter set. Statistical properties, such as mean number of base pairs, mean numbers of stacks, mean loop sizes, etc., are much less sensitive to the choice of parameter set and even of algorithm. Some features of RNA secondary structures, such as structure correlation functions, shape space covering and neutral networks, seem to depend only on the base pairing logic (GC or AUGC alphabet). Received: 16 May 1996 / Accepted: 10 July 1996 |
| Keywords: | Kinetic folding Minimun free energy structures RNA secondary structures Sequence structure relations |
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