Fat and fat-free mass were quantified using a Hologic Discovery (version 12.4; Waltham, MA, USA) enhanced-array dual-energy X-ray absorptiometer (DXA).
Thereafter, locked nucleic acid (LNA -enhanced arrays were used, based on the nucLNA -enhancedlogue LNarraysersen & wereel, 2003) with high affinity to RNA (Elkan-Miller et al, 2011).
To solve this problem, we build the generalized enhanced suffix array of our sequences, i.e. the enhanced suffix array of the concatenated sequence S : = S 1 $ S 2 where $ is a special character not contained the alphabet Σ; see also Babenko and Starikovskaya (2008) for a related approach.
Here, an enhanced suffix array is defined as a data structure 'consisting of the suffix array and additional tables'.
The last column indicates the number of PWMs one would need to search with in order to 'break-even' with the naïve method when taking into account the building time of the enhanced suffix array, (see supplementary material, text S1, for a more detailed comparison).
We refer to the troika of tables suf, lcp and skp as enhanced suffix array.
Ohlebusch and Gog [ 7] presented a solution for APSP using an enhanced suffix array.
Vmatch preprocesses the EST sequences into an index structure: an enhanced suffix array.
To handle these, we concatenate the single sequences with separator symbols, and construct the enhanced suffix array for the concatenation.
The construction of the enhanced suffix array took 33 minutes on a SUN UltraSparc III (900 MHz) CPU.
The algorithm to enumerate the lcp-intervals and singleton intervals, given the enhanced suffix array, runs in linear time, see [ 21] for details.
