• Multiple Alignment Sequence Editor of DNAMAN (MASED)
  • The Multiple Alignment Sequence Editor of DNAMAN (MASED) is an efficient tool for multiple sequence editing. You may use MASED to visualize multiple alignments and analyze sequence homology. The results of the Multiple Alignment function are loaded directly into MASED. You may also use MASED to analyze the multiple alignments produced by other programs such as GCG. MASED recognizes all multiple sequence formats listed in the pages 7-12. When you use the File | Open special | Multiple alignment command to open these files, DNAMAN loads them into MASED.



    1. Properties of MASED
    2. Press the Options button in MASED to open the property pages.

      In the Preferences page you may change the following properties of MASED:



    3. Functions of MASED
    4. There are many functions of MASED for sequence analysis and edting:

      - Shading homology regions

      - Changing list order

      - Moving a sequence fragment between gaps

      - Truncating aligned sequence fragments

      - Adding and deleting gap insertions

      - Exporting multiple sequences in different formats

      - Copying

      - Producing trees

      - Performing restriction analysis of DNA sequences

      - Predicting secondary structures of protein sequences

      - Comparison hydrophobic/hydrophilic properties of protein sequences



    5. Saving multiple alignment profile in MASED
    6. You may save the content of MASED, or export it to a text window. If you choose the File | Save menu, MASED will save the alignment in DNAMAN2 format. The saved multiple alignment profile can be retrieved and edited later.

      Output formats of multiple alignment in MASED

      Multiple alignment in MASED can be exported to a text window in any of the seven formats:

      There are some special options of exporting two sequence alignment (see the previous section).