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Related topics are listed below.
Customize the Look and Layout
Customize the Look and Layout
The following topics describe the many ways you can customize the look and layout of MegAlign Pro. Use the Style panel to change the look of a view (font styles and sizes, colors, number of decimal places, etc.) Customize the appearance and layout of…
Customize the appearance and layout of views
Customize the Look and Layout » Customize the appearance and layout of views
The following table lists ways in which you can customize the appearance and layout of views. Task How to… Show a view Use View > (View Name) > Show. Change the style (fonts, colors, calculation metrics and more) Use…
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…
Detect and remove outliers from the alignment
Perform a Multiple Sequence Alignment » Modify a multiple alignment » Detect and remove outliers from the alignment
After performing a multiple sequence alignment, you may wish to detect and remove outliers from the alignment. From the Distance view, select a reference sequence. Choose Distance > Order Sequences by Distance from Selection. By default, a heat map color scheme…
Part B: Replace a sequence in the Overview and view the phylogenetic tree
Perform a Multiple Sequence Alignment » Try it! – Perform a MUSCLE alignment with multi-segment sequences » Part B: Replace a sequence in the Overview and view the phylogenetic tree
In the Overview, look for the longest segment and the longest gap region (shown in gray) in each sequence. Note that both of these are located on the left for "Rat," and on the right for all the other groups. These clues indicate that the segments for "Rat" were likely…
Save the layout and apply it to other projects
Customize the Look and Layout » Save the layout and apply it to other projects
You can change the layout of MegAlign Pro’s views and panels as described in Customize the look and layout. Once you have arrived at a layout you like, you can save it and then apply it to future projects, either by default or only when you specify that it be…
Part D: Change metrics and rendering in the Distance view
Perform a Multiple Sequence Alignment » Try it! – Perform a Clustal Omega alignment » Part D: Change metrics and rendering in the Distance view
The Distance view shows a matrix (i.e., table) of numbers representing distances between each pair of sequences. Sequence distances are used as input in creating the Tree view, which you will explore in Part E. Selections within this view are synchronized with other…
Part C: Change sequence names and rendering in the Sequences view
Perform a Multiple Sequence Alignment » Try it! – Perform a Clustal Omega alignment » Part C: Change sequence names and rendering in the Sequences view
In Part B, you looked at the Sequences view while learning the function of the "viewport." You will now explore the Sequences view in more depth. The Sequences view displays entered sequences and aligned sequences. Sequences selected in this view are simultaneously…
Part E: Change the appearance of the Tree view
Perform a Multiple Sequence Alignment » Try it! – Perform a Clustal Omega alignment » Part E: Change the appearance of the Tree view
The Tree view shows evolutionary relationships predicted from the multiple sequence alignment. Click on the Tree tab at the bottom of the MegAlign Pro window. Press Neighbor Joining: BIONJ and then OK to calculate the tree. The Tree view is calculated using…
Choose the Alignment Type
Choose the Alignment Type
Which is better, multiple or pairwise alignment? This question is difficult to answer because it very much depends on how the alignment is going to be used. Mechanistically, the best sequence alignment is the one that produces the fewest number of mismatches. That…
Export the alignment report
Export » Export the alignment report
To export the alignment report for the selected block from a Mauve alignment, use File > Export Data > Alignment Report. To export the report for any other alignment type, use File > Export Data > Alignment Report. In both cases, the report is saved as a .txt file. …
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,…
Save, Close and Exit
Save, Close and Exit
The following table describes how to save files, close projects and exit from MegAlign Pro: Task How to… Save all of the open projects simultaneously Choose File > Save All or press Ctrl/Cmd+Shift+S. Each project is saved with an .msa…
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…
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…
Part D: View the phylogenetic tree
Perform a Multiple Sequence Alignment » Try it! – Perform a genomic alignment with Mauve » Part D: View the phylogenetic tree
*Note: The images in this section show examples of how the trees might appear. Your trees may have different arrangements or different branch lengths from the ones shown. The current names of each sequence originated from the accession numbers that were embedded in…
Part B: Navigate using the Overview
Perform a Multiple Sequence Alignment » Try it! – Perform a Clustal Omega alignment » Part B: Navigate using the Overview
Observe that the sequence blocks in the Overview are now the same lengths. Sequence gaps are represented by gray coloring within the blocks. The light blue vertical column shown at the left of the green blocks, above, is a "viewport" showing which region is…
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…
Multiple sequence alignment methods and options
Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Multiple sequence alignment methods and options
MegAlign Pro offers both gene-level and genome-level multiple sequence alignment algorithms. (Gene homology alignments are covered in a separate topic.) Gene-level alignment of either protein or nucleotide sequences: In general, the three gene-level aligners have…
Part A: Add and align sequences
Perform a Multiple Sequence Alignment » Try it! – Perform a Clustal Omega alignment » Part A: Add and align sequences
In this part of the tutorial, you will be adding 143 DNA sequences to the MegAlign Pro project and aligning them with the Clustal Omega algorithm using the default settings. If you have not yet downloaded and extracted the tutorial data, click here to download it.…
Save and reopen saved search results
Search for Sequence Matches » Save and reopen saved search results
To save the Table, Pairwise and Text views for the current search, use the Save as tool () in the top right of the Table view. The results are saved in .search format. To reopen saved results, choose Search > Open Search File and navigate to the .search file.…
Part F: Export the annotated target sequence
Features » Try it! – Map features » Part F: Export the annotated target sequence
In MegAlign Pro, hover over any target sequence annotation to read the entry. Verify that the sample entry matches your search criteria by checking the following: Is the feature a CDS? Does its original note contain the letters “RB”? Also observe…
Move the cursor to a specific position
Search » Move the cursor to a specific position
To go to a specified position: Choose Edit > Go To (Pairwise) Position, use Ctrl/Cmd+J. If the project contains only aligned or only unaligned sequences, type in a number and click OK. If the project contains a mixture of aligned and unaligned sequences,…
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…
Overview after aligning and entering additional sequences
MegAlign Pro Interface » Views » Overview » Overview after aligning and entering additional sequences
The Overview has different appearances, depending on the stage and workflow. In all cases, sequences are represented as either gray or colored blocks. Any sequence that is not part of an alignment is shown in solid gray. After performing an alignment, any new…
Part A: Add, rename and align sequences
Features » Try it! – Map features » Part A: Add, rename and align sequences
Before mapping features in MegAlign Pro, you first need to add and align the sequences. If you have not yet downloaded and extracted the tutorial data, click here to download it. Then decompress (unzip) the file archive using the method of your choice. If a…
Using the Overview as a sequence navigation tool
MegAlign Pro Interface » Views » Overview » Using the Overview as a sequence navigation tool
The light blue vertical column in the Overview is a “viewport” showing the region currently being displayed in the Sequences view. There are a number of methods—all performed within the Overview—for using the slider to navigate to a particular region in the…
Part C: View a genomic alignment in the Overview
Perform a Multiple Sequence 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…
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…
Part A: Add and align multi-segment files
Perform a Multiple Sequence Alignment » Try it! – Perform a MUSCLE alignment with multi-segment sequences » Part A: Add and align multi-segment files
If you have not yet downloaded and extracted the tutorial data, click here to download it. Then decompress (unzip) the file archive using the method of your choice. If a MegAlign Pro project is already open, choose File > New Alignment Project > Blank Document.…
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…
Try it! – Add and align multi-segment sequences
Sequences » Add multi-segment sequences to a project » Try it! – Add and align multi-segment sequences
The following video tutorial describes how to add multi-segment sequences and then align them using the MUSCLE multiple alignment algorithm. If you have not yet downloaded and extracted the tutorial data, click here to download it. Then decompress (unzip) the file…
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…
Try it! – Determine the strain of an experimental viral genome sample
Phylogenetic Trees » Try it! – Determine the strain of an experimental viral genome sample
In this tutorial, you will use MegAlign Pro to compare an experimental SARS-CoV-2 sample to references sequences from four SARS-CoV-2 strains in order to see which strain is present in the sample. This type of analysis can be used with any viral genome samples that…
Try It! – Align transcripts to genes using Local and Global pairwise alignments
Perform a Pairwise Sequence Alignment » Try It! – Align transcripts to genes using Local and Global pairwise alignments
This three-part tutorial illustrates the utility of pairwise alignments when comparing mRNA transcripts to their cognate genes. This example begins with multiple alignments of the alcohol dehydrogenase (ADH) gene from Drosophila melanogaster and four mRNA transcript…
MegAlign Pro Interface
MegAlign Pro Interface
MegAlign Pro displays your sequences and results in customizable views and panels. The items displayed in the window, their locations, colors, fonts, etc. can all be changed to suit your preferences. To learn more, see the following topics: Welcome screen…
Views
MegAlign Pro Interface » Views
The left side of the MegAlign Pro window is comprised of one or more “views.” To learn more about the types of views and how to change their appearances, click the links below. View types: Overview Sequences view Pairwise view Distance view Tree…
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…
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.…
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…
Sequences view
MegAlign Pro Interface » Views » Sequences view
The Sequences View displays added sequences and aligned sequences. Sequence names selected in this view are simultaneously selected all other views in MegAlign Pro. Similarly, sequence names selected elsewhere will be highlighted in the Sequences View. To access the…
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: Use a Global pairwise alignment method
Perform a Pairwise Sequence 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…
Phylogenetic Trees
Phylogenetic Trees
MegAlign Pro lets you create and display one or more phylogenetic trees for a multiple alignment. The trees can use different algorithms, or the same algorithm with different settings. To learn more, see the following topics: Generate a phylogenetic tree Get to…
Search for disagreements between sequences
Search » Search for disagreements between sequences
MegAlign Pro supports searching for positions where the same letter code does not occur in all sequences. This type of search looks only at IUPAC letter codes and ignores gaps. In other words, it will not look for positions in which one sequence has a letter code and…
Generate a phylogenetic tree
Phylogenetic Trees » Generate a phylogenetic tree
MegAlign Pro offers four tree-building algorithms: Neighbor joining: BIONJ uses the BIONJ algorithm (Gascuel, 1997), a variant of the Neighbor-Joining algorithm (Saito and Nei, 1987) that was used in classic MegAlign. Choose this option if your project includes…
Analysis Options screen
Perform a Gene Homology Alignment » Analysis Options screen
The Analysis Options wizard screen is the third of five screens used to set up a gene homology alignment. This screen allows you to customize options related to post-assembly analysis. You can leave all options at their default values or make custom selections, as…
Console panel
MegAlign Pro Interface » Panels » Console panel
The Console panel displays information, messages and warnings about the operation in progress, or an operation that was recently performed. To display the console for a particular project: Click the tab with the project name, then open its console using the View >…
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…
Panels
MegAlign Pro Interface » Panels
Settings panels allow you to optimize the look, contents and layout of the MegAlign Pro window. To learn what can be done within each panel and the expandable “sections” within each panel, click the links…
Search wizard: Options
Search for Sequence Matches » Search for sequence matches using BLAST » Search wizard: Options
The Options screen is the third of four screens in the sequence 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…
Trim an individual sequence
Sequences » Trim an individual sequence
Individual sequences in the project can be trimmed before or after alignment based on features or by direct selection. This is different from trimming the entire alignment, which affects all sequences in the project. To trim an individual sequence before or after…
Perform an initial multiple sequence alignment
Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment
To perform the initial multiple sequence alignment: Select three or more sequences to align, or select nothing if you want to align all sequences. (Note: If you choose just two sequences, or if only two are present, you will be prompted to instead do a pairwise…
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…
Features screen
Features » Map features (copy features to another sequence) » Features screen
The Features screen is the first wizard screen of the Map Features dialog, and allows you to choose the features you want to include or exclude in the mapping. *Note: This dialog is optional, and you may click Next, if desired, to skip to the next screen. However,…
Try It! – Follow a multiple alignment with Global pairwise alignments
Perform a Pairwise Sequence 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…
Part B: Use a Local pairwise alignment method
Perform a Pairwise Sequence Alignment » Try It! – Align transcripts to genes using Local and Global pairwise alignments » Part B: Use a Local pairwise alignment method
Now that you have finished Part A of the tutorial, this part shows how you can use a local pairwise alignment to resolve the correct mapping of the first intron in isoF and isoC. Click on Pairwise view tab. Look at the left drop-down menu at the top of the view…
Homologs view
MegAlign Pro Interface » Views » Homologs view
The Homologs view displays the results of a gene homology alignment. To access the view, perform a gene homology alignment. Then click on the Homologs tab or choose View > Homologs > Show. Use the dropdown menu at the top left of the view to choose whether to display…
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…
Tree view
MegAlign Pro Interface » Views » Tree view
The Tree view shows evolutionary relationships estimated from the multiple sequence alignment, and is calculated using the current tree-building algorithm and settings, and the currently-selected Distance metric. This view is only accessible after you have performed a…
Make a Selection
Make a Selection
Depending on the view, you can select one or more sequences, any portion of a sequence, or a specific portion of sequence corresponding to a feature. The active selection is highlighted in light blue. The selection can then be copied to the clipboard, copied in a…
Variants view
MegAlign Pro Interface » Views » Variants view
To see the Variants view, you must first perform a multiple alignment. When the alignment is complete, the Variants view opens showing a Compute Variants button. Click the button to calculate the variants. If you have specified a reference sequence, variants are…
Create a new project
Create or Open a Project » Create a new project
There are a variety of ways to create a new MegAlign Pro project, whether a blank project, one that is prepopulated with sequences, or even one that is prepopulated and with the alignment already in progress. *Note: To create a new project and add automatic…
Input Sequences screen
Perform a Gene Homology Alignment » Input Sequences screen
The Input Sequences wizard screen is the second of five screens used to set up a gene homology alignment. This screen is used to add the sequences that you wish to align to the reference. Add sequences from your local computer or the Cloud using any of the four Add…
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…
Assembly Output screen
Perform a Gene Homology Alignment » Assembly Output screen
The Assembly Output wizard screen is the fourth of five screens used to set up a gene homology alignment. This screen requires you to specify a project name. You can also change the location for the alignment output. Project name – Type a name for the…
Reference tracks
Tracks » Reference tracks
MegAlign Pro provides the option to specify a reference sequence and then use it to guide a MAFFT alignment or act as the comparison sequence for variant analysis. By default, the reference sequence is displayed as a track in the Overview and/or Sequences view headers.…
Run Assembly Project screen
Perform a Gene Homology Alignment » Run Assembly Project screen
The Run Assembly Project wizard screen is the fourth of five screens used to set up a gene homology alignment. This screen is used to specify a location in which to save temporary files and to start the alignment. You can also review system memory information that will…
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…
Remove features
Features » Remove features
While features can only be mapped when all sequences involved have been aligned, features can be removed from a sequence before or after aligning. Feature removal is not reversible, so use caution when removing features, especially those from non-consensus…
Research references
Appendix » Research references
Chou PY and Fasman GD (1978). "Prediction of the secondary structure of proteins from their amino acid sequence." Advances in Enzymology 47: 45-148. Darling AE, Mau B, and Perna NT (2010). “progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss, and…
Tracks panel
MegAlign Pro Interface » Panels » Tracks panel
The Tracks panel lets you manage the tracks displayed in the Overview and the Sequences view. To open the Tracks panel: Click on the Tracks tab (). If the panel is not already visible, reveal it using any of the following methods: Choose View > Tracks > Tracks…
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…
Set preferences
Appendix » Set preferences
To set preferences on Windows, choose Edit > Preferences. On Macintosh, choose MegAlign Pro > Preferences (macOS 12 and lower) or MegAlign Pro > Settings (macOS 13 and higher). Click any of the four items on the left to open the preferences dialog for that item, then…
Amphiphilicity (Eisenberg)
Tracks » Biophysics tracks » Amphiphilicity (Eisenberg)
The Amphiphilicity (Eisenberg) track predicts the Eisenberg Moment using the approach of Eisenberg et al., 1984. Hydrophobic moments are semi-empirical quantities based on computation and experimental measurements, which describe the distribution of hydrophilic and…
Specify a reference sequence
Sequences » Specify a reference sequence
This topic describes several reasons you might want to use a reference and procedures for specifying, changing, and removing the reference. Note that a reference sequence in MegAlign Pro is different from a reference in SeqMan Ultra or SeqMan NGen. In SeqMan NGen or…
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…
Set up local BLAST databases
Search for Sequence Matches » Set up local BLAST databases
In a typical sequence search, this application contacts the BLAST server at the National Center for Biotechnology Information (NCBI) and searches for sequence matches online. But what if your organization bans or limits online searches? Alternatively, what if you want…
Reference Sequence screen
Perform a Gene Homology Alignment » Reference Sequence screen
The Reference Sequence wizard screen is the first of five screens used to set up a gene homology alignment. You must input at least one reference sequence here before proceeding. To add one or more sequences from your computer: To add local sequences, press Add…
Pairwise alignment for sequences with similar lengths
Perform a Pairwise Sequence Alignment » Pairwise alignment for sequences with similar lengths
The following instructions describe how to align sequences with similar lengths (i.e., within one or two orders of magnitude). DNASTAR has used these pairwise algorithms in this workflow to successfully align protein sequences up to 35,000 bases in length. *Note: If…
Secondary Structure – Deleage-Roux
Tracks » Biophysics tracks » Secondary Structure – Deleage-Roux
The Secondary Structure – Deléage-Roux track predicts secondary structure using the approach of Deléage and Roux, 1987. The method uses an independent prediction of the protein’s structural class to bias the prediction of its secondary structure.…
Create a new project containing translations of nucleotide sequences
Create or Open a Project » Create a new project containing translations of nucleotide sequences
*Note: To create a new project and add sequences in their original formats, see the topic Create a new project. MegAlign Pro 17.6, released in 2024, can automatically translate selected nucleotide sequences (or subranges of those sequences) and add them to a new…
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…
Work with multiple trees
Phylogenetic Trees » Work with multiple trees
What are dynamic trees and how do they differ from “snapshots?”: MegAlign Pro allows you to compare multiple phylogenetic trees generated using custom settings. The phylogenetic algorithm you choose dictates which customizations affect the tree and whether…
Secondary Structure – Garnier-Robson
Tracks » Biophysics tracks » Secondary Structure – Garnier-Robson
The Secondary Structure – Garnier-Robson track , from Garnier et al. (1978), Garnier and Robson (1990), and Garnier, Gibrat and Robson (1996), predicts protein structure from the amino acid sequence. The method examines the propensity of a given residue to…
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.…
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…
When multiple features are selected
MegAlign Pro Interface » Panels » Details panel » When multiple features are selected
If two or more features have been selected in a track in the Overview or Sequences view, the Details panel contains the following information: Heading Number of features currently selected (in blue). Type – List of all feature types represented…
Clustal W alignment options
Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Multiple sequence 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…
Part A: Add genomic sequences using drag & drop
Perform a Multiple Sequence Alignment » Try it! – Perform a genomic alignment with Mauve » Part A: Add genomic sequences using drag & drop
If you have not yet downloaded and extracted the tutorial data, click here to download it. Then decompress (unzip) the file archive using the method of your choice. If a MegAlign Pro project is already open, choose File > New Alignment Project. Otherwise, launch…
Analyzing a gene homology alignment
Perform a Gene Homology Alignment » Analyzing a gene homology alignment
After a gene homology alignment has finished, you can view the results in the: Tree view — The phylogenetic tree was automatically calculated according to the algorithm you specified in the Assembly Output screen and is ready to view. Homologs view — This…
Print Images
Print Images
To print an image of any MegAlign Pro view, whether it is currently active or not: Choose File > Print or use Ctrl/Cmd+P. The Print Document dialog opens: Use the Printer drop-down menu to choose the desired printer from a list of available…
Favorites section
MegAlign Pro Interface » Panels » Places panel » Favorites section
The Favorites section is similar to the bookmarks folder for a web browser. It contains a list of previously-visited locations that you have decided you may wish to visit again. To access the Favorites section: Click on the Places panel expand bar entitled…
Pairwise alignment of a short sequence to a chromosome
Perform a Pairwise Sequence Alignment » Pairwise alignment of a short sequence to a chromosome
With the release of Lasergene 17.5 (July 2023), MegAlign Pro features a unique algorithm—adapted from one used in SeqMan NGen—that supports pairwise alignment of a short sequence (typically a cDNA) to a chromosome-length sequence. This type of alignment is…
Recent section
MegAlign Pro Interface » Panels » Places panel » Recent section
When you perform a search for a gene or numerical sequence location using Edit > Go To Position, each found location is automatically stored in the Recent section. Access this section by clicking on the Places panel expand bar entitled “Recent,” or by choosing View…
Merge unaligned sequences into an existing alignment
Perform a Multiple Sequence 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…
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…
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…
When a portion of a protein sequence is selected
MegAlign Pro Interface » Panels » Details panel » When a portion of a protein sequence is selected
When a portion of a protein sequence has been selected in any view (e.g., by double-clicking on a feature, or by dragging across the sequence with the mouse) except the Pairwise view, the Details panel contains the following information: Heading …
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…