Some genome browser tools such as the UCSC Genome Browser allow you to download a genomic sequence and specify introns as lowercase. pLOT can use this to automate annotating of exons from sequences formatted in this manner. See the example using NRF1.

pLOT has a number of tools for searching potential sequences of interest. Under the Tools menu, clicking the “DNA Elements Search Tool” menu (or pressing Ctrl+Alt+P) opens the Search window.

This windows allows for searching and annotating of potential:

• Bacterial Sigma70 promoter cores
• Shine-Dalgarno (bacterial ribosome binding) sequences
• Kozak signal
• Intron splice donor/acceptor (GT/AG and GC/AG)
• CAP binding sites
• Mef2 binding sites

The cutoff dropdown box can be used to set the stringency higher being more stringent and lower being less.

This tool can be accessed by clicking the Tools menu and the “Convert Bp to Codon” menu item. The user can input a base position manually (one at a time) or as a batch. If a project has a sequence, the input codons can be automatically added as features by clicking the “Annotate on Map” button. The default name for the features will be the amino acid in three letter code followed by the codon number. This can be changed in manual mode by entering a different name in the input box. In batch mode, names must be individually altered from the main window.

The default graphic and label color for added items is black. However, this can be changed by clicking the colored squares at the bottom and selecting a new color from the popup color selection window.

Added items can be placed at the bottom or top of the drawing order by selecting the Insert First/Last radio buttons respectively.

Clicking the “Cancel” button or hitting Escape will close the window, keeping any added annotations in the project.

This tool can be accessed by clicking the Tools menu and the “Convert Codon to Bp” menu item. As with the “Convert Bp to Codon” tool, the user can input a codon position manually (one at a time) or as a batch and the input codons can be automatically added as features by clicking the “Annotate on Map” button if a project has a sequence. The default name for the features will be “p.” followed by the amino acid in three letter code followed by the codon number. This can be changed in manual mode by entering a different name in the input box. In batch mode, names must be individually altered from the main window.

The default graphic and label color for added items is black. However, this can be changed by clicking the colored squares at the bottom and selecting a new color from the popup color selection window.

Added items can be placed at the bottom or top of the drawing order by selecting the Insert First/Last radio buttons respectively.

Clicking the “Cancel” button or hitting Escape will close the window, keeping any added annotations in the project.