R Exercise

Sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significa nce. In studying gene transcription regulation, splicing regulation etc, one important step is to identify sequence motifs.

1. Generate all possible DNA/RNA/PEPtide strings of a given length, for example, all possible 6mers, 7mers..etc.
2. Read DNA/RNA/PEP Sequence into R
3. Calculate the occurence frequency of the strings in the background reference and forground test sequences
4. Determine the over-representation/enrichment p-value
5. *Genome-scale analysis by looping over entries in string database