Extracting upstream regions in operons

This program outputs all potential upstream noncoding regions for an input set of genes. The algorithm starts by including the upstream region of the input gene. Then the algorithm checks the gene upstream of the input gene. If this second gene is likely to be part of the same operon as the input gene, then its upstream region will be included as well. The program outputs all intergenic regions upstream of a particular gene until an "operon head" is reached. An operon head is encountered when:

A divergently transcribed gene is encountered
Two tandem genes with separation greater than a certain value are encountered

Click here for a more detailed explanation of the method.

Enter genes to analyze:

Use operon prediction

Maximum distance between genes in the same operon:
Sequence to save upstream of each gene-- Min: Max:

No operon prediction

Exact length to take usptream of each gene:

Select genome:

Calculate upstream regions

Abigail Manson McGuire
Harvard Medical School Genetics Dept., Church Lab Alpert Bldg. 512 200 Longwood Ave. Boston, MA. 02115	Phone: (617) 432-0503 Fax: (617) 432-7266