This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. Show debugging information on the internal state of the search. Others can be specified.
Users can provide their own data files in their own directories.
Notes water is a true implementation of the Smith-Waterman algorithm and so produces a full path matrix. It therefore cannot be used with genome sized sequences unless you have a lot of memory and a lot of time. Warnings Local alignment methods only report the best matching areas between two sequences - there may be a large number of alternative local alignments that do not score as highly. You will be able to see this situation if you have done a dotplot and your local alignment does not show all the features you expected to see. A true Smith Waterman implementation like water needs memory proportional to the product of the sequence lengths.