FoldRNA predicts a single optimal secondary structure for an RNA molecule by the older method of Zuker. You specify the minimum stem length, minimum and maximum loop sizes, and the minimum number of bonds per stem. All loops or only the best loops can be displayed on your screen or written into a file. BestFit makes an optimal alignment of the best segment of similarity between two sequences. Optimal alignments are found by inserting gaps to maximize the number of matches using the local homology algorithm of Smith and Waterman.
Repeat finds direct repeats in sequences.
For word comparisons, the vertical sequence may not be more than 30,000-symbols long. No more than 200,000 points may be produced in the plot file. The point files can be quite large and should be deleted as soon as they have been examined. Window must be between 1 and 100, or if word comparison is done, the word size must be between 1 and 25. The points are the Cartesian coordinates of each point of similarity in units of the original sequence coordinates.