• DNAMAN Basics
  • This chapter provides the basic conceptions behind the DNAMAN software. It is important to understand these basics prior to performing sequence analysis.

    1. Sequence channels
    2. DNAMAN uses Sequence Channels to keep active sequences in the computer memory. The Sequence Channels increasing analysis efficiency by decreasing disk accessing time. Once a sequence is loaded into a Sequence Channel, you can perform many functional analyses, such as restriction analysis, translation analysis, sequence search and comparison and PCR primer design. There are twenty channels in DNAMAN, any of them can be chosen as Default Sequence Channel. Default sequence is the one you are currently working on. Click a number on the Sequence channel bar will activate the corresponding channel as default.

      Both DNA and protein sequences can be loaded into channels. DNAMAN checks the composition of a sequence to determine whether it is a DNA or protein fragment. DNA sequences are automatically loaded into channels. Protein sequences will be confirmed by users while DNA sequences will not. You may change the sequence type using the Analysis Definition function if sequence type is not correctly defined. The sequence in the default channel can be displayed in Info/Sequence bar.

    3. Menus
    4. DNAMAN has nine Main Menus that are displayed on the screen top. Each main menu has several menus, some of which have submenus. A command to carry out a function is described as a Main Menu | Menu | Submenu.

      Example:

      a) Choose the File |Open command to open a DNAMAN file.

      b) Choose the Sequence | Load Sequence | From Database command to load a sequence record from database into the default sequence channel.

    5. Tool bar
    6. The toolbar is designed for most frequently used menu commands and allow users to access them easily. You may show or hide the toolbar using the command in the Info | View Toolbar menu.

    7. Documents
    8. There are seven document types in DNAMAN.

      1) Text (Sequence) Document

      Sequence document is in general text format (Text Document). Text document is displayed in a Text window. DNAMAN provides a standard Text Editor for sequence editing. Sequences should be save as plain text file and the ".seq" extension should be added to the file name.

      2) Restriction Map Document

      Restriction map is used to save DNA maps(*.dmp). DNAMAN map file is in binary format and stores restriction map objects. DMP file can be only opened and edited with DNAMAN. You may also copy a DMP file as graphic drawing object to any other programs that accept drawings.

      3) Dot Matrix Document

      DNAMAN saves dot matrix data in binary DMF file that cannot be opened as text file .

      4) Multiple Alignment Document

      DNAMAN saves multiple sequence document in MSD (*.msd) format. MSD file is in text format with special keywords for Multiple Alignment Editor of DNAMAN (MASED). You can load MSD files in MASED and perform multiple sequence analysis. You may also open MSD files in text editor if necessary.

      5) Sequence Assembly Document

      Sequence assembly document is saved in SAF format (*.saf). SAF file is also in text format with special keywords for Sequence Assembly Editor of DNAMAN. Assembly editor is used to edit and visualize contigs. You may also open SAF files in text editor if necessary.

      6) Trace File Document

      DNAMAN can be used to view and analyze chromatogram files produced by automated DNA sequencing machines such as ABI series of PE BioSystem. DNAMAN can open ABI and SCF files, and also save edited sedquence to these files.

      7) Phylogenetic Tree Document

      DNAMAN saves phylogenetic tree file in text format with extension PTR. A Phylogenetic tree file can be opened or edited as text.