• Setting DNAMAN system configurations
  • Choose the Info | Settings command to set up DNAMAN system configurations.

    There are four pages to set the configuration parameters of Directory, DNA analysis, Protein analysis and others.

    Folder settings

    The folder settings are important in DNAMAN. The program may not functional properly if folders are not correctly set. There are six folders required in DNAMAN:

    1. DNAMAN system folder. All DNAMAN system files are stored in this folder. DNAMAN cannot work without this directory.

    2. Database folder. This is the folder where you can find all the databases.

    3. Multiple alignment folder. You may use this folder to store your multiple alignment data.

    4. Consensus data folder. DNAMAN keeps consensus data files in this folder.

    5. Default folder. DNAMAN starts always in this folder.

    All these folders must be correctly set up. You may change them by pressing the corresponding button and choosing an appropriate folder.

    DNA analysis settings

    DNAMAN uses some pre-set files for DNA sequence analysis. There are six file names in this page.

    1. Nucleotide property file. DNAMAN uses this file to display nucleotide properties.

    2. Enzyme file. This is the current restriction data file used in DNAMAN for restriction analysis.

    3. Annotation file. This file stores all sequence annotations recognized by DNAMAN. It is highly recommended not to change this file.

    4. Methylase file. DNAMAN uses also this file for restriction analysis, when dam and/or dcm methylations are involved.

    5. Search list file. This file contains your consensus sequence information for sequence search.

    6. BLAST template file. DNAMAN uses this file as template to generate BLAST document.

    You may modify these file names. However, you must be sure that the files exist, and contain correct information for sequence analyses.

    Protein analysis settings

    DNAMAN uses also some pre-set files for protein sequence analysis. There are five parameters in this page.

    1. Genetic code table file. This file contains all genetic tables. DNAMAN uses this file to find different genetic tables for translation analysis.

    2. Current genetic code table. This is the current genetic table used in DNAMAN for translation analysis.

    3. Amino acid property file. DNAMAN uses this file to display amino acid properties.

    4. Similar amino acid file. This file contains amino acid similarity matrix. DNAMAN uses this matrix to define the similarity between amino acids for alignment of two protein sequences.

    You may generate a new file for amino acid similarity by clicking the Generate Similarity Matrix button.

    You may modify these file names. However, you must be sure that the files exist and contain correct information for sequence analyses.

    Miscellaneous settings

    This page contains a few important settings of DNAMAN.

    1. Save channel information before exit. You may save existing channel information before the termination of current session of DNAMAN. When this option turned on, DNAMAN will keep all channel information for the next session of DNAMAN.

    2. MASED font. This is the default font for a MASED document.

    3. Print - Show page number. Check this option if you like to display the page number when you print out a document.

    4. Print - Show file name path. Check this option if you like to display the file information when you print out a document.

    You may modify all these settings according to your preferences.