How to Identify Bacterial Promoters Using MacVector

MacVector’s Subsequence tool is a very flexible search function that can be used for a variety of tasks. MacVector itself has a built-in variant of the function for maintaining and search primer databases (Analyze | Primer Database Search…). Each entry in the file MacVector uses as a source of subsequence data can have up to 3 segments, with variable length between the segments, along with a defined number of permitted mismatches and even a system for requiring that specific residues must match. That makes it ideal for searching for bacterial promoters. For example, the canonical Escherichia coli promoter sequence is a “-35” region TTGACA, then a gap of 16 to 18 residues, then a “-10” region “TATAAT”. You will find there is an EcoliPromoter.nsub file in the /MacVector/Subsequences/ folder. If not, you can download it. If you open the file in MacVector, you can see this.


You can see that the file has four entries – each of these has two segments representing the -35 and -10 region, but each has additional settings that control how close a match has to be before it is reported. The names give some idea of the stringency of the match – Perfect, Probable, Possible and Weak. If you double-click on the Probable item, you get this editor.

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