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