To get an idea of whether our method can be applied to large sequence sets, we have to consider the space requirement of the suffix array constructions in more detail.
Progress in the quest for an efficient suffix array construction algorithm started in 1993 with Manber and Myers [ 17] who applied a prefix doubling technique for repeat detection [ 18] to suffix array construction, obtaining an time algorithm for an input text of size n.
Importantly, 39% of the BN rat MHC genes (RT1n haplotype) annotated by Hurt and colleagues [16] were at the time point of array construction not represented in the Agilent database and therefore not represented on the Agilent whole rat genome array.
Probe synthesis and array construction was done in GeneFrontier Tokyo, Japann).
HH and WW carried out the tissue array construction and participated in the collection of clinicopathological data.
There are several linear time suffix array construction algorithms (SACAs) known in the literature.
The substantial savings in initial array construction are likely to be especially advantageous for microarray applications in which oligonucleotide quality control is the primary consideration.
We have implemented the alternative open source software tool mkESA, using the Deep-Shallow algorithm (Manzini and Ferragina, 2004) for in-memory suffix array construction instead of multikey quicksort as used by mkvtree.
MDJ participated in microtissue array construction and pathologic consultation.
With the uninitiated in mind, we provide an accessible exposition of the SA-IS algorithm, which is the state of the art in suffix array construction.
