MacMolly Tetra® Lite

Welcome

Welcome to MacMolly Tetra® Lite, the freeware version of Soft Gene's MacMolly Tetra® software package2 for analyzing and interpreting the sequence of biopolymers (DNA and Proteins).

Please read the license conditions (License.txt) before installing the software.

To download the most recent version of this software, or for information on the commercial version MacMolly Tetra® Pro, please visit our website: http://www.mologen.com

Installation

MacMolly Tetra® Lite runs with Apple MacOS 7.1 or higher. It comes in two versions, one for Macintosh 68K computers (MacMolly68K.sea),and one for Macintosh PowerPC computers  (MacMollyPPC.sea).To install on a specific machine, double-click on the respective file and follow the prompts for a target location on your computer.

Overview

The division of its rich functionality into separate modules is a key concept of MacMolly Tetra®. Each module is a stand-alone application that can be used either on its own, or in concert with the other modules.
The following modules are available in MacMolly Tetra® Lite:

Analyze

features functions like Editing and Listing sequences, Restriction Analysis, Translation & Backtranslation, Physical Properties, Design of PCR-Primers and of Hybridization Probes, and Import of foreign file formats

Interpret

contains the more interpretative (or, if you will, speculative) functions, like Secondary Structure Prediction, Hydropathy, Coding Probability, Repeats, Z-DNA, Binding Sites & Motifs, Composition and Distribution of monomers and oligomers, DNA Curving

Complign / Align

are all about Sequence Comparison and Alignment, including Multiple Alignments.
Complignuses a fast heuristic algorithm (similar to BLAST1) for sequence comparison and is hence best suited for comparison of similar sequences, especially DNA Sequences (e.g., when aligning both strands in double-stranded sequencing).
Align,on the other hand, uses a rigorous, computation intensive and consequently slower algorithm (Smith & Waterman3) for comparisons. It should be used for comparison of protein sequences for highest sensitivity (e.g., aligning phylogenetically distant proteins from the same protein family).

EMBL/GenBank DropSplit

is a simple utility program that converts a list of sequences resulting from database queries at the EBI or NCBI into the file format used by MacMolly.

Index of Functions

The following alphabetically sorted table maps the most important functions to the module that provides it:

Function Module
Alignment, Multiple Align, Complign
Alignment, Pairwise Align, Complign
Backtranslation (i.e. Peptide-> DNA) Analyze
Coding Probability of a DNA Sequence Interpret
Composition, monomer composition of sequence Analyze, Interpret
Confirm (read back) sequences Analyze
Convert TEXT files <-> MacMolly files Analyze
Curving of a DNA Interpret
Distribution of oligomers Interpret
Dot Plot (graphical pairwise sequence comparison) Align, Complign
Editing DNA, Protein sequence Analyze
EMBL, import multiple sequences  EMBL/GenBank DropSplit
EMBL, import single sequence  Analyze
GenBank, import multiple sequences  EMBL/GenBank DropSplit
GenBank, import single sequence  Analyze
Hybridization Probes Analyze
Hydropathy Interpret
Isoelectric Point (pI) Analyze
Listing a DNA or Protein sequence Analyze
Molecular Weight Analyze
Motifs, Search for Interpret
PCR Primers Analyze
Printing a DNA or Protein sequence Analyze
Repeats, direct, inverted Interpret
Restriction Analysis Analyze
Secondary Structure Prediction Interpret
Sequence Comparison Align, Complign
Tm of double-stranded DNA Analyze
Translate DNA -> Peptide Analyze
Translate Peptide -> DNA Analyze
Z-DNA prediction Interpret

References

  1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990). "Basic local alignment search tool." J Mol Biol 215(3): 403-10.
  2. Schöneberg, U., Vahrson, W., Priedemuth, U. und Wittig, B. (1993). Analysis and Interpretation of DNA and Protein Sequences Using MacMolly Tetra®. Bielefeld, KAROI-Verlag.
  3. Smith, T. and Waterman, M. (1981). "Identification of common molecular subsequences." J. Mol. Biol. 147: 195-197.