Genomic sequence tracts

Kuroda M, Yamashita A, Hirakawa H, Kumano M, Morikawa K, Higashide M, Maruyama A, Inose Y, Matoba K, Toh H, Kuhara S, Hattori M, Ohta T Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection. Proc Natl Acad Sci USA 2005 102 13272-13277. 

Schell MA, Karmirantzou M, Snel B, et al. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sd USA. 2002 99(22) 14422-14427. 

The availability of complete genomic sequences of probiotic strains belonging to the Lactobacillus and Bifidobacterium genera has paved the way to proteomic studies aimed at investigating probiotic functionalities. In fact, proteins directly mediate probiotic adaption to the harsh physical-chemical environment of the gastrointestinal tract (GIT), adhesion to host epithelial cells and intestinal mucosa, as well as probiotic health-promoting effects. 

The use of external lists of fc-mers is meant to provide the user with flexibility about the patterns to be considered. For example, the user may prefer to remove sequences of low complexity, such as polyA- or polyT-tracts, if it is known that such sequences are over-abundant and unlikely to be regulatory elements in the considered genomes. 

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