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====== Tools ======
===== Converting Uppercase to Exons =====
Some genome browser tools such as the [[http://genome.ucsc.edu/|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 [[Converting Uppercase to Exons Example|example using NRF1]].

===== DNA Element Search =====
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.

{{:elementtools_1.png?400|}}

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

For ribosome binding sites (Shine-Dalgarno and Kozak), optional minimum and maximum limits can be placed on the length of the predicted ORF to filter out unwanted results.

{{:elementtools_2.png?400|}}

The cutoff dropdown box can be used to set the stringency higher being more stringent and lower being less.
===== Converting Base Pair position to codon number =====
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 "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.

{{:bptocodon.png?400|}}

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.

===== Converting codon number to Base Pair position =====
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.

{{:codontobp.png?400|}}

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.
===== Converting an amino acid sequence to a DNA sequence =====
This tool can be accessed by clicking the Tools menu and the “Convert Amino Acid -> DNA” menu item.
A codon table can be selected using the dropdown box at the top of the window (Standard is the default table).

{{:aatodna_1.png?400|}}

Enter amino acid sequence in the text box below and click the "Convert" button.  The resulting DNA sequence will be generated and displayed in the text box at the bottom.  This sequence uses the most frequent codon for each amino acid for the specified codon table.

{{:aatodna_2.png?400|}}

Planned future options to this window includes filtering out restriction sites and adjusting for repeats, GC content and others.
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