Prediction of common secondary structures of RNAs by genetic algorithm Chen, Le, Maizel Jih-H Chen, Shu-Yun Le and Jacob Maize. Prediction of Common Secondary Structures of RNAs: A genetic Algorithm Approach, Nucleic Acids Res.,2000, Vol.28, No. 4 (991 - 999). rnaga rnaga perl "rnaga < params" 0 mv_files perl " ; mv fort.2 $seqfile.scr; mv fort.4 $seqfile.cm" 100 result_files *.scr *.cm params seqfile Sequence(s) 1 2 3 4 9 params perl "$value\n" 1 seqsfile perl 1 hcrtval Hcrtval: a structure is considered as a candidate of common structure during a GA iteration if the conservation score for the structure is no less than Hcrtval 0.8 If the program produces too many possible common secondary structures, such as 10**5, the computation cost for the second stage maybe huge. In this case, to reduce the computation time, you may want to increase the value of Hcrtval and/or decrease the value of beta. Also, in our experience the default value of beta can be 0.5. params perl " $value" 2 hcrtval2 Hcrtval2: a structure is taken as a common secondary structure by the program if the adjusted conservation score for the structure is no less than Hcrtval2 (Normally, Hcrtval2 < Hcrtval) 0.7 params perl ",$value" 3 pns pns: a criterion to make sure that the structure feature in a common structure is shared by majority of the sequences (pns = 0.6 means shared by at least 60% of the sequences) 0.6 params perl ",$value\n" 4 structures_nb Number of structures in a population params 200 A value of 100 is suggested for sequences of less than 100 nucleotides. perl " $value" 5 iterations_nb Number of GA iterations 100 params perl ",$value\n" 6 beta beta: a structure is considered as a candidate during a GA iteration if the free energy of the structure is no greater than (average random energy + beta * standard deviation) -1.5 increase this value by 0.5 each time if the program terminate with the message: No structure is sufficiently stable If the program produces too many possible common secondary structures, such as 10**5, the computation cost for the second stage maybe huge. In this case, to reduce the computation time, you may want to increase the value of Hcrtval and/or decrease the value of beta. Also, in our experience the default value of beta can be 0.5. params perl " $value" 7 zeta zeta: a structure is taken as a common structure if the free energy of the structure is no greater than (average random energy + zeta * standard deviation) -1.5 increase this value by 0.5 each time if the program terminate with the message: No structure is sufficiently stable params perl ",$value\n" 8 equivalency Parameters to determine the equivalency of two stems mxdp Stem position 3 params perl " $value" 9 mxdr Region size 3 params perl ",$value" 10 mxdL Loop size 3 params perl ",$value" 11 mxdrp Branches distance 3 params perl ",$value\n\n" 12