Shortest DNA Cyclic Cover in Compressed Space

For a set of input words, finding a superstring (a string containing each word of the set as a substring) of minimal length is hard. Most approximation algorithms solve the Shortest Cyclic Cover problem before merging the cyclic strings into a linear superstring. A cyclic cover is a set of cyclic strings in which the input words occur as a substring. We investigate a variant of the Shortest Cyclic Cover problem for the case of DNA. Because the two strands that compose DNA have a reverse complementary sequence, and because the sequencing process often overlooks the strand of a read, each read or its reverse complement must occur as a substring in a cyclic cover. We exhibit a linear time algorithm based on graphs for solving the Shortest DNA Cyclic Cover problem and propose compressed data structures for storing the underlying graphs. All results and algorithms can be adapted to the case where strings are simply reversed but not complemented (e.g. in pattern recognition).