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The techniques for pattern discovery use exhaustive search and can be used to detect possible sites of interest and assign putative structure or function to proteins.
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Several apriori-like algorithms were presented for solving it, such as generalized sequential pattern [34] and sequential pattern discovery using equivalence classes [35].
Analysis was performed by sequence alignment, by pattern discovery using SPLASH [10], [36], and by a combination of the two methods.
In the first step of periodic pattern discovery, we used a parameterized procedure that found the elementary periodic patterns for the values of parameter (p = 1, 2, 3, ldots ) that do not exceed a given threshold value.
The genome-wide repetitive fragments were also masked for the pattern discovery step using UCSC Genome Browser RepeatMasker annotation (http://www.repeatmasker.org).org
Thus large data sets may be stored in a relational database and may be extracted and preprocessed using SQL, and then visualization, statistical analysis and data mining or pattern discovery may be performed using tools that researchers are already familiar with.
This chapter discusses a recent Web-based tool called "GYM" that uses pattern discovery techniques.
Such alignments are commonly generated using pattern discovery software such as MEME [ 42].
Two studies (11%) by the same research group used pattern discovery to develop temporal models including SAPS II and SOFA data [ 8, 9] (Table 7).
In contrast to the Pattern Discovery Algorithm, our approach uses the generalized suffix tree annotated with the letters of the sequence alphabet.
For this purpose we used the pattern discovery tool from RSAT program to identify overrepresented hexa-, hepta- and octamer motifs in the 2 kb regions upstream from the putative translation start sites of the five genes.
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