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Related topics are listed below.
Set preferences
Appendix » Set preferences
To set preferences, choose Edit > Preferences (Windows) or MegAlign Pro > Preferences (Macintosh). Click any of the four items on the left to open the preferences dialog for that item, then follow the steps in the sections below. After setting preferences, click Apply…
Import an alignment from another application
Create or Open a Project » Import an alignment from another application
To import an alignment from another applicaton: Do either of the following: From the Welcome tab, click Open Project on the left. Then use the option Import alignment on the right. Choose File > Import Alignment. Navigate to the file you wish to…
Change the default application for opening files
Appendix » Change the default application for opening files
Windows 7 and Windows 8: Open the Control Panel. Go to Programs > Default Programs > Associate a file type or protocol with a specific program. Select extension you wish to change in the Extensions list and then click the Change program button. Click the…
Part D: Map a filtered set of features
Features » Try it! – Map features » Part D: Map a filtered set of features
In this example, you will map only CDS features which have a note containing the letters RB. Right-click on the name of the source (upper) sequence and select Features > Map Features to Bottom Sequence. The Map Features wizard launches. In the Features…
Export a tree to a tree viewer
Export » Export a tree to a tree viewer
To export a phylogenetic tree to a file: Use File > Export Data > Tree to export tree data in Newick (.newick) or Nexus (.nex, .nxs) formats . The saved file can be opened by several free and commercial evolutionary biology software programs. To set the default…
Installed Lasergene file locations
Appendix » Installed Lasergene file locations
The following file names use ‘x’ to represent the version number. File Category Application Path Application2 ArrayStar Windows: C:\Program Files (x86)\DNASTAR\Lasergene x\ArrayStar SeqNinja (command line) Windows:…
Change the default print size
Print Images » Change the default print size
Unless otherwise specified on your computer, the default printing size for all DNASTAR applications is “U.S. Letter” size (8.5 × 11 inches = 21.6 × 28 cm). You can temporarily change to another size, such as A4, from within the application. However, the…
Turn off usage logging
Appendix » Turn off usage logging
By default, usage logging is enabled for Lasergene. To opt in/out of usage logging: Launch the DNASTAR Navigator. Use whichever of the following commands is available; the command varies by Lasergene version and operating system. Window > Preferences…
Access ID dialog
Search for Sequences Online » Access ID dialog
As of December 2018, NCBI requires an API key for faster access to NCBI services, or to run more searches concurrently. To get a key, start by setting up an NCBI account. After registering your account, click on your user name and request your key using API Key…
Jobs panel
MegAlign Pro Interface » Panels » Jobs panel
After initiating an NCBI BLAST or Entrez search, you can monitor its progress and download its eventual output from the Jobs panel. This panel is not visible in a project until you have started running at least one search. To open the Jobs panel: Do any of the…
Search wizard: Job
Search for Sequences Online » Search for sequence matches (BLAST) » Search wizard: Job
The Job screen is the fourth of four screens in the BLAST Search wizard, This screen allows you to overwrite the default search name with a custom name and initiate the BLAST search. The text box contains an automatically-generated name for the search job. If you…
Clean cached files on startup
Appendix » Clean cached files on startup
Prior to the Lasergene 14.0 release, the default MegAlign Pro startup ran a “-clean” option. This option automatically removed some cached files on application restart. The “-clean” option is no longer executed at each startup. However, if you are a Windows…
Search for Sequences Online
Search for Sequences Online
This application lets you search National Center for Biotechnology Information (NCBI) databases for matches to text or sequence that you specify. Query part or all of a nucleotide or protein sequence against one of NCBI’s sequence databases using the Basic…
Create or Open a Project
Create or Open a Project
Before you can add sequences to a project and align those sequences, you first need to create a MegAlign Pro project. If you already have a project from MegAlign Pro (or its predecessor, MegAlign), you can also open that to view or make changes. For details about each…
Advantages of using SeqNinja files
Sequences » Advantages of using SeqNinja files
SeqNinja is DNASTAR’s tool for advanced and batch editing of genome sequences and features. SeqNinja allows you to convert file formats, batch edit and export features, merge and split sequence data, and transfer features between genome versions, automating the…
Export an image of the view
Export » Export an image of the view
To export an image of a view : Choose File > Export Image > (View Name) or click the Export image tool ( ) at the upper right of a view that allows exporting. Specify the file name and choose the export format: Adobe PDF (.pdf), Microsoft…
Search for text or accession number matches (Entrez)
Search for Sequences Online » Search for text or accession number matches (Entrez)
The Entrez Search wizard is used to search a text query or accession number against NCBI’s Entrez databases for nucleotides or proteins. To launch the Entrez search dialog, choose Search > Text Search in > NCBI Nucleotide or Search > Text Search in > NCBI…
Search wizard: Search
Search for Sequences Online » Search for sequence matches (BLAST) » Search wizard: Search
The Search screen is the second of four screens in the BLAST Search wizard. The Search screen is used to choose the BLAST program and database. Specify whether you wish to search for Nucleotides or Proteins. Select the desired BLAST program from the Using…
Search wizard: Options
Search for Sequences Online » Search for sequence matches (BLAST) » Search wizard: Options
The Options screen is the third of four screens in the BLAST Search wizard, and has two tabs: Selection and Matches. These tabs allow you to customize miscellaneous parameters relating to the BLAST search. Click the Selection tab to make it active. In the…
Troubleshoot the error “A different version is running”
Appendix » Troubleshoot the error “A different version is running”
If you receive the error “A different version of Lasergene is running” when you try to launch a Lasergene application, but another version of Lasergene actually isn’t running, there may be a lingering .state file from another version that needs to be…
Mapping features in MegAlign Pro vs. SeqNinja
Features » Map features (copy features to another sequence) » Mapping features in MegAlign Pro vs. SeqNinja
The ability to map features exists in both MegAlign Pro and DNASTAR’s SeqNinja. Here are some reasons you might want to map features in one application versus the other: Task Use MegAlign Pro Use SeqNinja View the alignment and the mapped…
Notes regarding multiple alignments
Perform a Multiple Alignment » Perform an initial multiple alignment » Notes regarding multiple alignments
When performing a multiple alignment, take the following tips into consideration. Sequence order matters: The order in which sequences appear in the Overview and Sequences view may affect the results of the multiple sequence alignment. If you are not satisfied with…
Welcome to MegAlign Pro
Welcome to MegAlign Pro
MegAlign Pro is Lasergene’s application for generating multiple and pairwise alignments of protein and/or nucleic acid sequences using your choice of alignment methods. Easily navigate between synchronized views with a click of a button, and rearrange views and…
Try it! – Perform a MUSCLE alignment with multi-segment sequences
Perform a Multiple Alignment » Try it! – Perform a MUSCLE alignment with multi-segment sequences
Sequences that consist of more than one chromosome, contig, or fragment are called multi-segment files. Suppose you want to string together the consensus sequences from all the contigs in an assembly, or chromosomes in a genome, or exons in a gene, etc. If you enter…
Copy, Paste and Delete
Copy, Paste and Delete
In many cases, once you have selected text, data, sequences or subsequences, you can copy the information to the clipboard. *Note: Copy functions are limited by application memory and operating system buffer size. Therefore, for very long sequences or subsequences,…
Part C: Map all features
Features » Try it! – Map features » Part C: Map all features
In this part of the tutorial, you will map all features from the source sequence to the target sequence. Right-click on the name of the source (upper) sequence and select Features > Map Features to Bottom Sequence. The Map Features wizard launches. In the…
Sequence alignment vs. sequence assembly
Welcome to MegAlign Pro » Sequence alignment vs. sequence assembly
Sequence alignment and sequence assembly are very different workflows, but the terms are often used incorrectly. Adding to the confusion, both workflows can involve an optional “reference” sequence, and both can use some of the same sequence file types.…
Subalign sequences
Perform a Multiple Alignment » Modify a multiple alignment » Subalign sequences
While sequences such as full-length calmodulin proteins typically align well throughout the entire length of the polypeptides, full-length alignments of other sequences may not generate such neat blocks of similarity. For example, multiple sequence alignments of…
Part C: Use a Global pairwise alignment method
Perform a Pairwise Alignment » Try It! – Align transcripts to genes using Local and Global pairwise alignments » Part C: Use a Global pairwise alignment method
Since the Local pairwise alignment in Part B was not an improvement over the multiple alignments in Part A, you will now try a Global pairwise alignment. This type of alignment forces the ends of both sequences to be aligned. Click the gear icon on the Pairwise view…
Details panel
MegAlign Pro Interface » Panels » Details panel
The Details panel shows details of the application, selection or project. To open the Details panel: This panel is represented by a blue “information” icon (). If the panel is not already visible, reveal it using any of the following methods: Choose View >…
Customize the layout of other window components
Customize the Look and Layout » Customize the layout of other window components
Controls for this application’s view, panels and expand bars are described in the following table. For information that pertains only to views, also see Customize the appearance and layout of views. Task “How To” Show or open a hidden…
Part B: Perform a Mauve alignment using modified parameters
Perform a Multiple Alignment » Try it! – Perform a genomic alignment with Mauve » Part B: Perform a Mauve alignment using modified parameters
In this part of the tutorial, you will explore how to view and change parameters prior to performing a multiple sequence alignment. Choose Align > Align Using Mauve and align the sequences using the default parameters. Because this is a genomic alignment, the…
Rename sequences manually
Sequences » Rename sequences manually
To manually rename a selected sequence: Select a single sequence name from any MegAlign Pro view, then right-click on it and choose Rename Sequence(s). Alternatively, select the sequence name and choose Edit > Rename Sequence(s). The Choose Label dialog opens…
Filter search results
Search for Sequences Online » Filter search results
After doing a BLAST or Entrez search, the Table view shows a list of potential matches. To filter this table to include only matches that meet additional criteria, click the Filter results tool () in the header and then click Filter. This opens the Filter dialog. The…
Add only the portion of sequence that corresponds to a feature
Sequences » Add only the portion of sequence that corresponds to a feature
This topic describes two methods that allow you to align only the portions of sequences the correspond to a particular gene or other feature. Other portions of the sequences are discarded or removed prior to alignment, making the alignment for that gene both faster and…
Overview section
MegAlign Pro Interface » Panels » Style panel » Overview section
To access options affecting the Overview display, click on the Style panel expand bar entitled Overview, or choose View > Style > Overview. Task How to… Increase/decrease the amount of vertical space between sequence blocks Use the…
Add only sequences that meet filtering thresholds
Sequences » Add only sequences that meet filtering thresholds
You can specify a group of sequences to add and then use filtering options to only add a subset of those to the project. To add only sequences that meet filtering thresholds: Open the filter dialog by doing any of the following: From the Welcome screen, select New…
Part E: Compare output files
Features » Try it! – Map features » Part E: Compare output files
When the mapping initiated in Part D is finished, click the hyperlink to the output directory. Open both All features_map_features_1_report.tsv and CDS-RB features_map_features_1_report.tsv in any suitable spreadsheet…
Align selected unaligned sequences with an existing alignment
Perform a Multiple Alignment » Modify a multiple alignment » Align selected unaligned sequences with an existing alignment
In some cases, you may have already aligned sequences, then decide to completely realign the same sequences plus certain selected unaligned sequences. To align selected unaligned sequences with an existing alignment: Add sequences to the project and align some or…
Clustal Omega alignment options
Perform a Multiple Alignment » Multiple alignment methods and options » Clustal Omega alignment options
The Clustal Omega algorithm is for gene level alignment of either protein or nucleotide sequences. To run a Clustal W alignment, select two or more sequences and choose Align > (Re)Align Using Clustal Omega. If you wish to change method options, instead choose Align >…
Overview
MegAlign Pro Interface » Views » Overview
The Overview provides a way to navigate within the sequences, no matter what type of sequences or alignment is used. In the case of genomic alignments generated by Mauve, the Overview also allows you to explore the relationships between multiple aligned blocks.…
Merge unaligned sequences into an existing alignment
Perform a Multiple Alignment » Modify a multiple alignment » Merge unaligned sequences into an existing alignment
To merge unaligned sequences into the current project’s existing alignment: In contrast to the “Profile alignment” method, this method retains existing gaps, and adds new gaps, if necessary. Add sequences to the project and align some or all of…
Export data from the Text, Table or Pairwise views
Export » Export data from the Text, Table or Pairwise views
The Export data tool ( ), located in the header above the Text, Table or Pairwise views, lets you export data from those views. This tool provides a choice of three options, one of which has four sub-options. Options include: Export Data > Matches…
Merge two existing alignments (“Profile alignment”)
Perform a Multiple Alignment » Modify a multiple alignment » Merge two existing alignments (“Profile alignment”)
To merge two existing alignments: A “profile alignment” occurs when you merge a MegAlign Pro alignment (.msa) that was saved earlier with the current project. Profile alignments merge two existing multiple alignments without removing any of the existing gaps.…
Distance section
MegAlign Pro Interface » Panels » Style panel » Distance section
The Distance section affects the appearance of the Distance view. To access this section, click on the Style panel expand bar entitled Distance, or choose View > Style > Distance. *Note: In Lasergene 17.1 and earlier, this section was used to specify distance…
Table view
MegAlign Pro Interface » Views » Table view
To access the Table view, perform a BLAST search. When the search is complete, the Text, Table and Pairwise views are displayed together in a single popup window that is separate from the main MegAlign Pro window. To reopen all three views at a later time, click on the…
Search wizard: Query
Search for Sequences Online » Search for sequence matches (BLAST) » Search wizard: Query
The Query screen is the first of four screens in the BLAST Search wizard. The Query screen is where you add the query sequence, i.e., the sequence for which you wish to locate matches in the NCBI BLAST database. At the top of the screen, next to “Search…
Rename sequences automatically using specified data fields
Sequences » Rename sequences automatically using specified data fields
The following procedure lets you create labels for one or more selected sequences automatically, using specified fields such as sequence length, organism, or description. To rename sequences using specified data fields: Select one or more sequence names from any…
Sequence section
MegAlign Pro Interface » Panels » Style panel » Sequence section
To access options affecting the Sequences view and Pairwise view, click on the Style panel expand bar entitled Sequences, or choose View > Style > Sequences. Task How to… Select font options for the ruler numbers in the view Use the…
Overview after aligning multiple genomes with Mauve
MegAlign Pro Interface » Views » Overview » Overview after aligning multiple genomes with Mauve
The Overview has different appearances, depending on the stage and workflow. A Mauve genome alignment results in a set of locally colinear blocks (LCBs), each of which is a conserved region across multiple sequences. In MegAlign Pro, these may be referred to as…
Create a new MegAlign Pro project
Create or Open a Project » Create a new MegAlign Pro project
To create a new MegAlign Pro project: Do any of the following: From the Welcome tab, click New Project on the left. Then choose one of the options on the right: New blank alignment project – Opens an empty project window. New alignment…
Perform a Pairwise Alignment
Perform a Pairwise Alignment
This application supports local, global and semi-global pairwise alignment methods. Pairwise alignments can only be performed when two sequences, and only two sequences, have been selected. A common workflow is to first perform a multiple alignment on an entire group…
Tracks
Tracks
“Tracks” are rows of information that can be displayed or hidden, as desired, in the Overview and Sequences view. Tracks can pertain to a header, footer, or individual sequence row. The following video provides a brief overview of how tracks are used in…
Part C: View a genomic alignment in the Overview
Perform a Multiple Alignment » Try it! – Perform a genomic alignment with Mauve » Part C: View a genomic alignment in the Overview
Once the alignment has finished, notice how the Overview has changed in response to the parameter change, including changes to the colors of the blocks, and differences in which blocks are hanging below the line (i.e., on the opposite strand). Locate the…
Add multi-segment sequences to a project
Sequences » Add multi-segment sequences to a project
Sequences that consist of more than one chromosome, contig, or fragment are called multi-segment sequences. By entering a group of sequences into MegAlign Pro using a special command, the entire data set will be concatenated end-to-end and treated as a…
Welcome screen
MegAlign Pro Interface » Welcome screen
The Welcome “project” opens when you launch MegAlign Pro and is a central location for opening projects, searching NCBI databases, getting help, and much more. As you add projects, the Welcome “project” will remain as the leftmost tab unless you…
Part A: Compare results from three multiple alignment methods
Perform a Pairwise Alignment » Try It! – Align transcripts to genes using Local and Global pairwise alignments » Part A: Compare results from three multiple alignment methods
This part of the tutorial demonstrates that if you don’t have annotations to rely on for validating multiple alignments, a pairwise alignment is a good alternative. This tutorial uses a default MUSCLE alignment of the Drosophila melanogaster ADH gene and the…
Substitution matrices
Perform a Pairwise Alignment » Substitution matrices
A substitution matrix describes the rate at which a nucleotide or amino acid changes to another nucleotide or amino acid over time. When performing a pairwise alignment, you can specify the desired substitution matrix in the (Pairwise) Alignment Options…
Style panel
MegAlign Pro Interface » Panels » Style panel
The Style panel has expandable sections with options affecting the Overview, Sequences, Distance and Tree views, as well as multiple and pairwise alignments. To open the Style panel: Click on the Style tab (). If the panel is not already visible, reveal it using any…
Tree section
MegAlign Pro Interface » Panels » Style panel » Tree section
To access options affecting the Tree view, click on the Style panel expand bar entitled Tree, or choose View > Style > Tree. Task How to… Specify the layout of the view Click on any of the four orientations to show the phylogenetic…
Clustal W alignment options
Perform a Multiple Alignment » Multiple alignment methods and options » Clustal W alignment options
The Clustal W algorithm is for gene level alignment of either protein or nucleotide sequences. To run a Clustal W alignment, select two or more sequences and choose Align > (Re)Align Using Clustal W. If you wish to change method options, instead choose Align > Align…
Generate a phylogenetic tree
Phylogenetic Trees » Generate a phylogenetic tree
To generate a new phylogenetic tree: Add sequences and perform a multiple alignment. Use any of the following methods to direct MegAlign Pro to create a tree using the algorithm you specify. For helpful advice on choosing the best tree for your data, see this…
MAFFT alignment options
Perform a Multiple Alignment » Multiple alignment methods and options » MAFFT alignment options
The MAFFT algorithm is for gene level alignment of either protein or nucleotide sequences. If you want to align a large number of sequences in MegAlign Pro, we recommend using this algorithm. As of the Lasergene 17.3 release (August 2021), MegAlign Pro uses MAFFT7.…
Change the order of sequences
Sequences » Change the order of sequences
Whether preparing an image of a view for publication, or simply for ease of analysis, you may want to change the order of sequences in one or more views. For instance, you may wish to order the tree to create a pleasing image or to draw the viewer’s focus to a…
Try It! – Use Local pairwise alignment to find a gene within a genome
Perform a Pairwise Alignment » Try It! – Use Local pairwise alignment to find a gene within a genome
Consider the case of a researcher who is trying to investigate the role of a gene isolated from a yet-unsequenced Salmonella strain. This strain has already been demonstrated to be both copper and multi-drug resistant. As demonstrated in the following tutorial,…
Try It! – Follow a multiple alignment with Global pairwise alignments
Perform a Pairwise Alignment » Try It! – Follow a multiple alignment with Global pairwise alignments
This tutorial demonstrates a situation in which a pairwise alignment can help resolve a confusing placement of gaps within a multiple alignment. In this case, a multiple protein sequence alignment suggests that the protein sequence from a specific organism (Tupaia…
Multiple Alignment section
MegAlign Pro Interface » Panels » Style panel » Multiple Alignment section
To access options affecting the display of multiple alignments in the Sequences view, click on the Style panel expand bar entitled Multiple Alignment, or choose View > Style > Multiple Alignment. Task How To Designate the sequence to consider…
Pairwise view
MegAlign Pro Interface » Views » Pairwise view
The Pairwise view displays sequences after performing a pairwise alignment or a BLAST or Entrez database search. Sequence names selected in this view are simultaneously selected all other views in MegAlign Pro. Similarly, sequence names selected elsewhere will be…
Pairwise Alignment section
MegAlign Pro Interface » Panels » Style panel » Pairwise Alignment section
To access options affecting the display of pairwise alignments in the Pairwise view, click on the Style panel expand bar entitled Pairwise Alignment, or choose View > Style > Pairwise Alignment. Task How To Specify the wrapping style for rows…
Distance view
MegAlign Pro Interface » Views » Distance view
The Distance view shows a matrix (i.e., table) of numbers representing distances computed for each pair of sequences for the selected aligned block. Sequence distances are used as input in creating the phylogenetic tree shown in the Tree view. Selections within the…