## DNA_analysis

Click here for the genetic code.

This window is a command tool. It acts on either:

- the active sequence window
- all the sequences listed in the currently active keyset if you press the Search active Keyset button. That button is a toggle and turns RED when activated.

Searches on the dna result in coloration of the sequence, which shows on the bases and amino acids (if visible) and on the yellow strip.

### Menu items:

- Quit: quits the window.
- Help: brings up this help.
- Print: prepares a Post Script file in ./PS which you can then print on your local laser printer.
- Finger print: Restricts with the enzymes used for the C.e. physical map hindIII and sau3aI. You get prompted for the name of a file where the result of the search may be exported. The sites are shown in 2 colors in the feature window.
- Restriction Key_Set: Will import a list of restriction enzymes that can then be searched for in the active sequence or KeySet of sequences.
- Restrict Site Text-editor: Searches for AA motifs or Bases restriction sites. You can give the sequence you search for or the name of a set of known restriction enzymes, (list the class Restrict to see them). The sites are shown in the sequnce window, and recorded at the end of the Dnacpt window. The use of ambiguous letters such as R is allowed To activate the search type return. Try also the Show Gel Button.
- Dump Sequence: If UseKeySet is set, dumps in fasta format all sequences of the active keyset (or selection list). Else, dumps in fasta format the active region of the active sequence window, e.g. you can fasta dumps bases 3800 to 7000 of a given sequence.
- poly R/ poly Y: looks for 12 or more contiguous AG or TC segments, and prints out the result of the search. This is equivalent to search for a restriction of 12 R or 12 Y (r is a-g, y: t-c), but the print out is more precise.
- Splice Concensus: Gives the 5' and 3' splice concensus sequences around the introns exons boundaries in the sequences of the active keyset. The result is shown in the Dnacpt window itself. Resize the window to see it.
- Codon Usage: Gives the codon usage in the sequences of the active keyset. The result is shown in a new window. Note that the genetic code is recalled in the next page of this help.
- Lengths: Gives the histogram of the lengths of the individual sequences in the active KeySet.
- Show Gel: Pops a Gel Tool with its own help page.
- Clear: Clears the Dnacpt window, useful before using Splice concensus or restrict buttons.

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last edited: July 1994