DNAmend analyzes DNA-sequences and manipulates them. You can find restriction sites, open reading frames and certain sequence patterns, translate the sequences and display them in different formats, perform Restriction, Ligation or End modification on-line. You may export maps of your DNA-sequences into Graphic software to prepare them for publication.
The features of DNAmend shall make
the program a useful tool for people,who are concerned with DNA-cloning.
We tried to create a PC routine, that provides on-line control on some
steps of a cloning protocol - including the selection of the vectors and
fragments, their processing by restrictase digestion, subsequent ligation,
and the analysis of the cloned DNA.
© Copyright: Bjoern Maul & Piet Jonas 1999
The program runs on IBM-compatibles
(at least 368, 4 MB RAM) under
Microsoft Windows 3.x, Windows 95, and Windows NT.
DNAmend automatically recognizes whether
a file is not of the DNAmend-file format. When you try to open such a file,
DNAmend makes the offer to import the DNA sequence information of the file
In principle, you can import DNA sequences of any PC text format. The program
interprets the characters A,T,G,C, and U as symbols for the respective
nucleobases. As these characters of course are either present as letters
in the accompanying text that precedes or follows the actual sequence information
in most of the sequence file types, you must select the actual sequence
information before you open a file which is not of the DNAmend-file format.
You can find a base sequence of choice
inside of an entire DNA sequence and display it in the sequence file window
by running the Search command. Put the base sequence that is to
be searched for into the text box Search for. Of the dialog box
Search. Use the ambiguity code if you want to. For your convenience,
it is listed under the text box. You can monitor the search by clicking
the command button Search. DNAmend displays the search results in
the list box Result and directly in the active window.
The text box main sequence contains the sequence of the NON-coding strand of your DNA fragment in 5´-3´ direction. If you are editing linear DNA, you can circularize it by activating the check box circular. You can only close the DNA sequence, if it does not contain start or end sequences.
The Menu View
...displays the NON-coding strand of your DNA sequence as a single strand in 5´-3´-Richtung. Restriction sites are green. Search results are red. Translation is blue.
...displays your DNA sequence as a double strand with the NON-coding strand on top in 5´-3´-direction. Restriction sites are green. Search results are red.
...creates a map of your DNA sequence. The name of the sequence is placed on top of it. Under the sequence is a scale for the length in base pairs. If your sequence is circular, the ends of the scale are connected by a broken line and the ends of the sequence have small arrows. In this case you either can display a circular map of the sequence. Restriction sites are marked, provided that you selected enzymes. Search results appear as red tags, markers are displayed as arrows under the sequence.
...creates a map of a circular DNA sequence. The name of the sequence is placed in the middle of the circular molecule. Tags at the sequence mark the base position. Restriction sites are marked, provided that you selected enzymes. Search results appear as red tags, markers are displayed as arrows within the molecule circle.
DNAmend translates your DNA sequence into a peptide sequence according to the universal genetic code. You have the choice to display each of the three possible reading frames seperately or all of them simultaneously. Moreover, you can decide whether you want to display all amino acids or some selected only, and whether DNAmend shall show biochemical short names or the single letter code.
DNAmend can select restriction enzymes to be associated with the sequence in the active window. On the basis of this selection you can subsequently create a restriction map or cut your DNA sequence.You select the enzymes in the dialog box Select enzymes. DNAmend offers a data base with a large collection of restriction endonucleases, which can be supplemented with your personal entries. If you save your DNAmend-file, the current selection of enzymes is saved together with the sequence, and is recalled when you open the file the next time.
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