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Query: UMLS:C0027960 (mole)
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A computer program is presented which determines the secondary structure of linear RNA molecules by simulating a hypothetical process of folding. This process implies the concept of 'nucleation centres', regions in RNA which locally trigger the folding. During the simulation, the RNA is allowed to fold into pseudoknotted structures, unlike all other programs predicting RNA secondary structure. The simulation uses published, experimentally determined free energy values for nearest neighbour base pair stackings and loop regions, except for new extrapolated values for loops larger than seven nucleotides. The free energy value for a loop arising from pseudoknot formation is set to a single, estimated value of 4.2 kcal/mole. Especially in the case of long RNA sequences, our program appears superior to other secondary structure predicting programs described so far, as tests on tRNAs, the LSU intron of Tetrahymena thermophila and a number of plant viral RNAs show. In addition, pseudoknotted structures are often predicted successfully. The program is written in mainframe APL and is adapted to run on IBM compatible PCs, Atari ST and Macintosh personal computers. On an 8 MHz 8088 standard PC without coprocessor, using STSC APL, it folds a sequence of 700 nucleotides in one and a half hour.
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PMID:Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. 169 21

Computer programs written in BASICA (IBM'S VERSION OF BASIC) language were developed for the calculation of the gas exchange parameters of CO2 assimilation, leaf conductance, stomatal conductance, residual conductance, intercellular CO2 concentration, transpiration, water use efficiency and transpiration ratio in an open system. Formulas are discussed in both an algebraic and in a BASIC computer program form. Calculations based on mole fractions of CO2 and water vapor are explained and both molar and mass fluxes are included in the program output to facilitate comparisons with data from the literature. Corrections are made in the program to account for under-estimation of CO2 assimilation due to the increase in flow rates out of sample chambers caused by simultaneous transpiration. A sample output is included to illustrate the formatting capability of the program.
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PMID:A BASIC computer program for calculation of photosynthesis, stomatal conductance, and related parameters in an open gas exchange system. 2444 23