Gene promoter regulatory element analysis computational methods and their use in transgenic applications

A system for identifying regulatory elements, comprising:

• a computer;
• an article of software executing on the computer, the article of software adapted for performing steps of:
• (a) receiving a first orthologous species sequence;
• (b) receiving a word length;
• (c) receiving a relative offset;
• (d) receiving at least one additional orthologous species sequence, wherein each of the orthologous species sequences is associated with a species, and each of the species is an orthologous species;
• (e) performing a pairwise comparison between each pair of orthologous species sequences;
• (f) computing overlapping portions of the sequence overlapping the sequences of all of the orthologous species sequences within the relative offset and greater than or equal to the word length;
• (g) providing an output to a user identifying the overlapping portions of the sequence for all of the orthologous species sequences to identify candidate regulatory elements.

A computer-assisted method of identifying regulatory elements, comprising:

• receiving a first sequence;
• receiving a word length;
• receiving a relative offset;
• receiving at least one additional sequence;
• performing a pairwise comparison between each pair of sequences;
• computing using a computing device, overlapping portions of the first sequence overlapping the sequences of all of the sequences within the relative offset and greater than or equal to the word length;
• providing an output to a user identifying the overlapping portions of the first sequence for all sequences to identify candidate regulatory elements.