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 input files structure and on what can be calculated with MB. The list below represents the items of "Analysis" menu. Additional programs (plugins) can be launched from "plugins" menu. For more detailed information, algorithm explanations please refer to "mbhelp.pdf". If you want to add a DNA sequence to database, please refer to "add_howtos.txt" in the DATABASE directory.

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 acids 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 acids 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 ACIDS 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). If you do not want to register the program, then it is still possible to see the list of available updates here
    If you want to develop your plugin for MB please read this document.
    MALIGN.DLL
    Description: Hierarchical Multiple Sequence Alignment
    Input: a valid DNA/amino acids sequence
    Output: multiple alignment, phylogenetic tree

    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.stud.uni-karlsruhe.de/~uzbar