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:
  1. A divergently transcribed gene is encountered
  2. 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:

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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