Secondary Structures for Individual Sequences

The input file format for both programs is fairly simple. An input file contains one or more sequences. A sequence must appear as a single line in the file without embedded white spaces. A sequence may be preceded by a special line starting with the character followed by a sequence name. This name is used by RNAfold as the root name for the postscript output files for this sequence. 

You can check the content of the file marry. seq using the command cat or 

Of course you can create the input file with your favorite text editor, such as emacs or vi. Windows and Mac users beware if you use a word processor (such as MS Word) you must save the file as plain text, no tin the word processor s native file format. (Otherwise your file will be garbled by the word processor s formatting information ) 

The last line of the text output contains the predicted MFE structure in bracket notation and its free energy in kcal mol-1. A dot in the bracket notation represents an unpaired position, and a base pair (i, j) is represented by a pair of matching parentheses at positions i and /. 

Compute the MFE structure and additional equilibrium ensemble properties  

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