Prokaryotic Transcriptional Regulator Binding Sites

[thackel]

Hello All,

I am trying to identify the following LytTR variable consensus sequence [TAC][AC][AC]GTTN[TAG][TG] in the Staphylococcus aureus subsp. COL complete genome as an imperfect direct repeat and was wondering which sequence finder would be most appropriate. Some of the options that I have attempted have such as pattern locator and fuzznuc did not permit variable sequence inputs using the traditional bracketed nomenclature. I am an undergrad and inexperienced in bioinformatics so extremely explicit directions would be incredibly appreciated as I recognize it is likely not a deficiency in the programs I am using but incorrect inputs. Thank you,

Taylor

[kmcarr]

Hi Taylor,

Could you explain a bit more what you mean when you say 'fuzznuc did not permit variable sequence inputs using the traditional bracketed nomenclature.'? Perhaps I am misunderstanding, but fuzznuc does permit bracketed bases to indicate variable matching bases at a position. For example here is a pattern I use regularly with fuzznuc.

>ViromePrimerB <mismatch=1>
<[GT]TNNCCCA[GT]TCAC[GT]ATC

I have my fuzznuc patterns stored in .pat files with the file specifier given as the argument to the -pattern option on the command line.

What is happening when you try to run fuzznuc?