DNAMAN provides various functions for DNA translation and protein sequence analyses. Seven different genetic code tables are available for translation analysis. You may also add user defined genetic codes to the list. Translation overview may help you to visualize graphically the locations of open reading frames. You may calculate amino acid composition of a protein sequence, estimate its isoeletric point, plot its hydrophobic/hydrophilic profile and predict its secondary structures.
You may choose one of genetic code tables for translation analysis. Universal code is the most used in translation analysis for all biological species. However, in some case you may need to work with a special genetic code for specific works, such as translating yeast mitochondrial DNA to protein.
DNAMAN provides seven genetic code tables for your choice. In addition, you may create your own genetic code for your work. You may select any of these codes as the default genetic code. The default genetic code will be used in all functional analyses concerning sequence translation.
Choose the Protein | Select Genetic Code Table command to open the Genetic Code Table selection box. All available codes are listed in the box. Click the code name to select it as default code.
You may add a new genetic code table or edit an existing one by clicking the Edit button in the Genetic Code Table selection box. The table file is in text format. You may edit it according to your preference. However, there are some rules to make DNAMAN correctly use this file. To add a new code table:
1.Start with “//” in the first line.
2.Type the code name in the second line.
3.Enter the table. Use one letter codes for amino acids, lowercase letter for start codon, * for stop codon. You can define up to five start codons and five stop codons in a genetic code table. The code order should follow the standard universal genetic code table from top to bottom, from left to right.
You may visualize the genetic table by choosing the Info | Genetic Code Table command. DNAMAN displays the universal genetic code table and some variations.
A. Universal code
B. Vertebrate mitochondrial code
C. Yeast mitochondrial code
D. Insect mitochondrial code
E. Protozoa mitochondrial code
F. Plant mitochondrial code
G. Ciliate protozoa nuclear code
To facilitate the searching for ORFs on a large DNA sequence, DNAMAN provides a graphic presentation of translation overview on the six reading frames of the current DNA sequence. With the overview, you may easily locate the translation start and stop positions. However, the overview cannot give correct prediction when introns are present.
In the graph, the top straight line represents DNA sequence. This line is equally divided into ten parts as scale. Six diagrams are used to represent the six reading frames of the sequence and each line represents one of them. On each diagram, the Initial codons are shown as short vertical lines above each sequence line and the Stop codons shown under the sequence line. The top three diagrams show the reading frames on Plus (sense) strands and the bottom three diagrams show the Minus (anti-sense) strands. The names at left indicate the Reading Frames.
Since translation initial and stop codons vary with different genetic code tables, the diagrams will change when you select another genetic code table.
You may change the location and length of the diagrams. Place the cursor on the right end of the first line. When the cursor switches to , press the left mouse button and drag it to change the length of the diagrams. To move the diagrams, place the cursor on the left end of the first straight line (scale). When the cursor switches to , press the left mouse button and drag the diagrams to another location.
When the cursor is a cross on the overview graphics, the position coordinate is displayed on the left corner of the screen.
There are two methods to display sequence coding information from the Overview:
You may modify the Overview graph by pressing the Options button. A dialog box appears to show the options.