OpSearch

From NMPDR Wiki

The operon search displays genes from a single genome in operon order. Genes that are reasonably close to each other on the same strand are displayed in sequence order, each with its attendant upstream region. The purpose of the search is to assist the process of finding new operons and identifying their regulatory sites. The search form includes the standard Genome Control and Gene Display Options. For the purposes of this search, only one genome can be selected, so the genome control does not include all its special buttons and selection controls.

The following parameters can be used to tune the search.

• Specify the Maximum distance between operon genes to control how close together two genes have to be in order to be considered as part of the same potential operon. This distance is only used for adjacent genes on the same strand. Genes on different strands always break the chain.
• Specify the Upstream base pairs to display to control how much upstream DNA is displayed in the last column of the result table.
• Specify the Instream base pairs to display to control how much DNA from the beginning of the gene is to be displayed after the upstream DNA. The upstream DNA is shown in upper case; the instream DNA is shown in lower case.
• Specify the Maximum lint size to place a lower limit on the size of genes to be considered. A gene with fewer base pairs than the maximum lint size will be discarded as noise.