MegAlign offers researchers a choice of four pairwise and four multiple sequence alignment methods for aligning nucleic acid or polypeptide sefquences. Users can enter their own sequences or load public data directly from NCBI. To find more related sequences for alignment, a BLAST query can be run or the Entrez text query interface can be utilized, followed by dropping in the sequences wanted from the list of matches.

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Alignments views can be customized to highlight the similarities or differences of the sequences. Differences in chemical, structural or functional characteristics between sequences, researchers groupings or consensi can be displayed. researchers can construct phylogenetic trees, generate detailed numerical reports or export data of sequence comparisons. MegAlign provides valuable tools permitting comparisons of gene families or sequence pairs that can be customized for presentations and publications.

MegAlign Features

• Sequence Entry
• Import data from many popular file formats
• Read sequences and features from other Lasergene project files
• Edit template sequence and share newly created features through integration with SeqBuilder and other Lasergene modules
• Download sequences from NCBI* using accession number, BLAST or text search


• Alignments and Analyses
• Align DNA, protein and DNA + protein sequences
• Perform multiple sequence alignments using:
  • Multiple Sequence Alignments:

    Method	Advantages	Disadvantages	Applications
    ClustalV	very fast may handle end-gaps better than ClustalW	alignment not as accurate as ClustalW – slow, accurate	aligning many DNA and protein sequences irrespective of relationships creating preliminary alignments to optimize subalignments for ClustalW refinement
    ClustalW – fast approximate	fast	might not be as robust as ClustalW – slow, accurate	same as ClustalV
    ClustalW – slow, accurate	most accurate method for typical alignments	might not handle end-gaps optimally slow	same as ClustalV popular method for refining alignments for phylogenetic analysis
    Jotun-Hein	alternate to Clustal facilitates tests of robustness of predicted phylogenies fast	not recommended when sequence relationships are uncertain lower capacity than Clustal not intended for DNA alignments	aligning modest numbers of closely related, short to moderate length proteins

  • Pairwise Alignments:

    Method	Advantages	Disadvantages	Applications
    Wilbur–Lipman	fast	not as accurate as Martinez–Needleman–Wunsch may be better if there are many long sequences	DNA alignments
    Martinez–Needleman–Wunsch	more accurate than Wilbur–Lipman	slow	DNA alignments
    Lipman–Pearson			protein alignments
    DotPlot method	apply to DNA and protein alignments		DNA alignments protein alignments

• Create sub-alignments from selected ranges of longer alignments
• Reconstruct phylogeny
• Calculate sequence similarity and distance
• Edit an adjust final alignment manually if desired
• Export data and alignment into popular formats


• Graphical Displays and Tools
• Customize alignment displays
• Highlight matches or mismatches to the consensus or other sequence with distinct colors or shading
• Define the consensus by residue or by chemical, structural or charge characteristics
• Create a custom consensus based on researcher’s own residue classification scheme
• Display consensus strength as color-coded histograms
• Copy selected sections of alignment report and paste into other applications



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• Bootstrapping
• Bootstrapping is a process that compares phylogenetic trees generated from similar alignments and counts the number of times a specific branching pattern occurs. Those counts appear on the branches expressed in percentage terms. The branch with higher values are statistically more alike.
• Bootstrapping is used to test for consistency and robustness of a tree created using a Clustal method.
• Bootstrapping can provide a measure of the robustness of a feature of the data dependent upon the chosen criterion for comparison.

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Lasergene is a leading software tool used by molecular biologists in a wide range of sequence assembly and analysis applications. Through its cross-application design, users can easily share much of their data and synchronize updates to quickly be able to observe the results of their experimentation.

Lasergene is a suite of 7 different modules, each of which is provides users with unique sequence analysis capabilities. Researchers are able to search and retrieve sequences using integrated BLAST and Entrez tools.

• Assemble E. coli size and larger genomes — Enhancements to the SeqMan Pro assembler now permit users to assemble genomes equivalent or larger than E. coliwith a modest desktop computer.
• Assemble large Expressed Sequence Tag (EST) and Single Nucleotide Polymorphism (SNP) data sets and other projects requiring extensive depth of coverage analysis. SeqMan Pro has been improved to more accurately perform large depth of field coverage EST and SNP projects.
• Read 454 Life Sciences^TM output files (*.sff, *.fna, .fas and *.qual types) Pyrosequencing techniques offered by 454 Life Sciences offer the most established applications in this area. Researchers can import file formats directly from 454®, use along with Sanger sequencing methods and take advantage of the analysis tools of Lasergene.
• Maximum Expected Coverage — The Maximum Expected Coverage is a user defined depth of coverage expected in the assembly. Once sequences are assembled, areas exceeding the value are designated by a thick red line in the Strategy view.
• View Flowgram diagrams for 454® assembly visualizations — Flowgram diagrams using *.sff output can be generated (below). Base calls and Quality scores for each call are shown within the histogram.
• Increase in speed of the module in performing small and large assemblies. Lasergene 7.2 allows users to assemble large bacterial genomes using 454 Life Sciences pyrosequencing methods. Flowgrams are available to view the assembly and Quality Scores can also be shown in the histogram. The newest module, is the tool that permits assembly of sequences into contigs from a wide range of project sizes. Editing can be performed to eliminate poor quality data and contaminating data to give better final results. SeqMan Pro uses DNASTAR’s unique Trace Quality Evaluation system for generating consensus sequence calls. Lasergene version 7.1 is the first that allows users to work with both traditional Sanger data and data generated by next-generation technologies such as 454®. Assemblies exceeding 600,000 in size have been successfully performed with SeqMan Pro using 454® data.

MegAlign, is used primarily to generate pairwise and multiple sequence alignments of DNA and/or protein. A wide range of analytical algorithms are available for these alignments, giving you the flexibility needed in your work. Additional information can be obtained by going to the DNASTAR website and looking at the Lasergene Information Sheet.

SeqBuilder is the module that enables users to edit nucleic acid and amino acid sequences and to view the sequences in seven different ways, including linear and circular maps. Because SeqBuilder is integrated into most other Lasergene modules, edits are shared automatically with other applications.

GeneQuest helps users in identifying and annotating coding regions and other features of interest in your DNA sequence. It aids in the location of genes and regulatory elements. Once methods have been applied results can be displayed graphically.

PrimerSelect is the module used to design primers and probes for PCR, sequencing, transcriptions and hybridization experiments. You can analyze oligos from either those resulting from your input parameters or have a sorted list of possible primers created for DNA, RNA or back-translated protein templates. Users can manipulate parameters, edit primers preview the primer edit’s effects on sites and coding note conditions for ideal annealing conditions.

Protean is the protein structure prediction module of Lasergene. It can be used to predict and display patterns, secondary structural characteristics and physiochemical properties of proteins using a comprehensive library of analytical methods.

EditSeq is provided with every Lasergene system to enable you to work on nucleic acid and protein sequences of all sizes from a variety of formats, including GenBank, FASTA, MacVector, GCG®, Text, ABI®, and data from the clipboard. You can even access NCBI's databases by accession number or utilizing the integrated internet interface to search BLAST and Entrez text databases.

DNASTAR has been a pioneer in working with large and small academic institutions alike to bring state-of-the-art sequence analysis to the classroom. Over the last decade, hundreds of instructors from around the world have made Lasergene part of their standard curriculum by taking advantage of DNASTAR's free educational software offer. This program is designed to assist small programs that focus primarily on the training of students verses research to utilize advanced sequence analysis tools.

Depending on the institution’s needs, DNASTAR's educational system offer is available for one semester at a time. It provides the laboratory with a full suite of Lasergene that can be used with either Windows or Mac platforms. It is a fully functional, full Lasergene suite including all seven modules of the latest version of the software.

If you believe that your institution may qualify, click Free Educational Software, to be directed to the form on our website that will gather your contact information, course information, and the software products you plan to install to assist you in teaching the basics of DNA and protein sequence assembly and analysis to students in your class.

A DNASTAR representative will contact you to provide specific details and determine your eligibility. In addition, before DNASTAR ships the software, the department chair will need to sign a license agreement for the product you plan to use in your class — Lasergene. Please contact DNASTAR if you have additional questions.