MB Version 6.8x


Program Guide for the First-Time Users


Q: Why this guide?
A: MB 6.8x includes many tools for DNA analysis, so it may be a little bit complicated to start using the program to analyze DNA sequences. This guide should give the user quick information on the structure of the input files and on what can be calculated with MB. The list below represents the items of "Analysis" menu. Additional programs (plugins) can be launched from the "plugins" menu. For more detailed information, algorithm explanations, questions about how to add new sequences to the database please refer to "mbhelp.pdf".

Q: How can I start the program?
A: Normally, just click on "MB DNA Analysis" link from your desktop/program group, you can also execute "mb.exe" from the main directory of the program.
When analyzing bigger datasets with many sequences, splitting saved sequence data into several directories is a good idea. In the main folder of the program you will find a small application called "startmb.exe", placing it with the restriction enzymes' database file ("resenz.dat" in the "database" directory of the program) into the folder with your data and executing it, will let the program consider only the data present in that specific directory. This will make the data management a lot easier and will also let you create several restriction profiles (one in each directory). For further information please consult the manual.

Changes in this version

Included Features of MB:

  • Restriction Analysis
    Input: a valid nucleotide sequence in *.prt files in database directory (help on how to import your sequence: please see "add_howtos.txt" for more information).
    Results: base-count, restriction sites positions, melting point calculation for DNA, restriction map, plasmid/linear DNA drawing
  • Protein Analysis
    Input: a valid nucleotide sequence in *.prt files in database directory (help on how to import your sequence: please see "add_howtos.txt" for more information).
    Results: translation, amino acid count, disulfide bridges count, chemical properties of protein calculation, codon usage, prediction of the secondary protein structure.
  • Molecular Weight Calculator
    Input: a valid nucleotide sequence in *.prt files in database directory (help on how to import your sequence: please see "add_howtos.txt" for more information).
    Results: Calculation of the molecular weight for double-/single-strand DNA in g/mol
  • Dotplot
    Input: a valid nucleotide or amino acid sequence in the database directory (help on how to import your sequence: please see "add_howtos.txt" for more information).
    Results: Dotplot graph with alignment data
  • Open Reading Frame (ORF) Search
    Input: a valid nucleotide sequence in *.prt files in database directory (help on how to import your sequence: please see "add_howtos.txt" for more information).
    Results: positions of the ORFs
  • Isoelectric Point (pI) Calculation
    Input: a valid AMINO ACID sequence. If the user has got only a DNA file, it is possible to create a corresponding AA sequence using "Sequence Translator"-feature in "Extras"
    Results: protein charge graph as a pH function
  • Primer design
    Input: 5'-3' primer sequence.
    Results: melting point calculation, hybridisation, self-hybridisation, homology search
  • Additional Programs (Plugins)
  • The program files can be found in the "PLUGINS" directory (*.DLL files). They will be automatically recodnized by the main application. You can launch these programs from "Plugins" menu tab within the MB's interface

    To download new plugins or update the installed versions please use automatic update function (you will have to register the program, see here). Otherwise please check regulary the official homepage to make sure not to miss some important updates. If you want to develop your own plugin for MB please read this document.
    MALIGN.DLL
    Description: Hierarchical Multiple Sequence Alignment
    Input: a valid DNA/amino acid sequence
    Output: multiple alignment, phylogenetic tree
    HELIX.DLL
    Description: General alpha-helix analysis tool (draws spirals and calculates the hydrophobicity graph)
    Input: a valid amino acid sequence
    Output: helix graph, hydrophobicity graph
    RepMan
    Description: RepMan is an advanced report managing utility for MB. You can easily import image/text data from the main application for further editing.
    Input: in any report window of MB, right-click on your mouse and look for "Export to RepMan" option. Clicking on it will transfer your data to RepMan

    If you still have unanswered questions, please write to the developer at: mb-dna@gmx.de
    Author, Developer, Ideas, Design, Technical Support: Oleg Simakov
    Contact information:
    MB Homepage: http://www.molbiosoft.de