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Try it! – Map features
Features » Try it! – Map features
Both MegAlign Pro and SeqNinja allow you to copy a single annotation, or all annotations from a source sequence to a target sequence. During the process, you may optionally filter features so as to include or exclude specific gene types. In this tutorial, you will…
Try it! – Perform a Clustal Omega alignment
Perform a Multiple Sequence Alignment » Try it! – Perform a Clustal Omega alignment
This tutorial will use the Clustal Omega algorithm to multiply align 143 DNA sequence files consisting of regional variations of the Human Papilloma Virus L1 gene (HPV-L1). HPV has affected humans for hundreds of thousands of years and is known to cause cervical…
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…
Try it! – Perform a genomic alignment with Mauve
Perform a Multiple Sequence Alignment » Try it! – Perform a genomic alignment with Mauve
In this tutorial, you will be adding six nucleotide sequences to MegAlign Pro using drag & drop, and then aligning them with the Progressive Mauve algorithm. Drag and drop is a feature available in all Lasergene applications, and is useful for entering multiple…
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…
Try it! – Perform a MUSCLE alignment with multi-segment sequences
Perform a Multiple Sequence 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…
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…
Try It! – Use Local pairwise alignment to find a gene within a genome
Perform a Pairwise Sequence 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,…
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…
Perform a Multiple Sequence Alignment
Perform a Multiple Sequence Alignment
MegAlign Pro supports the following multiple sequence alignment methods: Clustal Omega, Clustal W, MAFFT, MUSCLE and Mauve. Click here for descriptions and a comparison of the different methods. To learn how to perform, modify, and troubleshoot multiple sequence…
Perform a Pairwise Sequence Alignment
Perform a Pairwise Sequence Alignment
MegAlign Pro supports local, global, semi-global, and chromosome-based pairwise alignment methods, as well as a specialized proprietary method for aligning cDNAs or other short sequences to a chromosome. Click here for descriptions and a comparison of the different…
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…
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…
MegAlign Pro Tutorials
MegAlign Pro Tutorials
MegAlign Pro tutorials appear in the table of contents just under corresponding help topics. In addition, each tutorial is also listed below. Miscellaneous tutorials: Add and align multi-segment sequences Map features Multiple alignment…
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…
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…
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…
Part A: Compare results from three multiple alignment methods
Perform a Pairwise Sequence 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…
Troubleshooting “fatal error” in Clustal Omega alignments
Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Troubleshooting “fatal error” in Clustal Omega alignments
Clustal Omega requires that each sequence in an alignment contain at least one residue that is not an ambiguity code. DNA sequences must contain at least one A, C, T or G. RNA sequences must contain at least one A, C, U, or G. Protein sequences must contain at…
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.…
Choosing a pairwise alignment method
Perform a Pairwise Sequence Alignment » Choosing a pairwise alignment method
MegAlign Pro has four pairwise alignment algorithms. Align to Chromosome: DNASTAR is used to perform individual pairwise alignments of 1 to 25 short sequences (typically cDNA sequences) to a chromosome-length reference sequence. This method was released with…
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…
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…
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…
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…
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…
Compute Variants
Compute Variants
After performing an assembly, MegAlign Pro can calculate variants between other sequences and the currently-specified reference sequence, or between all sequences and the consensus. For instance, you might download an annotated reference sequence that you found online…
Numeric tracks
Tracks » Numeric tracks
A numeric track displays a plot of values along one or more sequences in the project. To display numeric tracks: The visibility of numeric tracks in the Sequences view is dependent on: The origin of the project. For example, the Model ‘n’ Cα Distances…
Visually Compare Other Sequences to One Sequence
Visually Compare Other Sequences to One Sequence
You can visually compare sequences in the alignment to one of the aligned sequences by using settings in MegAlign Pro’s Style panel to highlight differences or matches. By default, the comparison is against the reference sequence, if you have specified one.…
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…
Features panel
MegAlign Pro Interface » Panels » Features panel
The Features panel lets you specify which feature types should be visible in the Overview and the Sequences view once a sequence has been expanded. To open the Features panel: Click on the Features tab (). If the panel is not already visible, reveal it using any of…
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…
Manually specify sequence type
Sequences » Manually specify sequence type
When you add a sequence to a project, MegAlign Pro uses clues in the sequence file to ascertain whether it is DNA, RNA or protein. When uncertain, it will prompt you to supply the missing information as you add the sequences. If MegAlign Pro guesses incorrectly…
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…
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…
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,…
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…
Explorer panel
MegAlign Pro Interface » Panels » Explorer panel
The Explorer panel is used to control which phylogenetic tree is displayed in the Tree view, and allows you to create additional trees or delete them. To open the Explorer panel: Click on the Explorer tab (). If the panel is not already visible, reveal it using any…
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…
Trees section
MegAlign Pro Interface » Panels » Explorer panel » Trees section
The Trees section of the Explorer panel is used to control which phylogenetic tree is displayed in the Tree view, and allows you to create additional trees or delete them. *Note: If you are instead seeking information on the Tree section of the Style panel, click…
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: Map a single feature
Features » Try it! – Map features » Part B: Map a single feature
In this part of the tutorial, you will map a single selected feature from the source sequence to the target sequence. In order to choose the appropriate mapping command, you will need to know where the source and target sequences appear in relation to one another in…
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…
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…
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…
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…
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…
Places panel
MegAlign Pro Interface » Panels » Places panel
The Places panel lets you quickly navigate to a sequence location or range that you have visited before. The following video shows how to bookmark favorite locations using the Places panel: To open the Places panel: Click on the Places tab (). If the panel is not…
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…
Generate a phylogenetic tree
Phylogenetic Trees » Generate a phylogenetic tree
MegAlign Pro offers three 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…
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,…
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…
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…
Hydropathy – Kyte-Doolittle
Tracks » Biophysics tracks » Hydropathy – Kyte-Doolittle
The Hydropathy – Kyte-Doolittle track predicts regional hydropathy of proteins from their amino acid sequences, using the approach of Kyte and Doolittle, 1982. Hydropathy values are assigned for all amino acids and are then averaged over a user-defined window. The…
Retain custom names during export
Export » Retain custom names during export
After using File > Rename or File > Rename with Fields, the custom names are only exported as part of the sequence data in certain cases. Raw data sequences imported into MegAlign are never modified in any way, and always retain their original names. The following…
Open an existing project
Create or Open a Project » Open an existing project
To open an existing MegAlign Pro project (.msa): Do any of the following: From the Welcome tab, click Open Project on the left. Then use the options on the right to Open alignment project or open a recent document. Drag an .msa file from the file explorer…
Add translations of nucleotide sequences to a project
Sequences » Add translations of nucleotide sequences to a project
In MegAlign Pro 17.6 and later, you can add nucleotide sequences to an existing project as translated amino acid sequences. This functionality can be useful when you have DNA and protein sequences that you want to align together. MegAlign Pro does not support the…
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…
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…
Navigate between projects
Create or Open a Project » Navigate between projects
You can open multiple projects within a single instance of MegAlign Pro. Each project is displayed in a separate tab and is initially assigned a unique name (Untitled[#].msa). To make a project the active project: Click on its project tab. To open an additional…
Search for nucleotide or residue strings
Search » Search for nucleotide or residue strings
MegAlign Pro supports searching for strings of nucleotides or residues that match a typed query of IUPAC code letters. By default, the search tools are hidden. To display them, click on the Search tool () in the upper right of most views. This causes the search tools…
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…
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…
Hydropathy – Hopp-Woods
Tracks » Biophysics tracks » Hydropathy – Hopp-Woods
The Hydropathy – Hopp-Woods track predicts protein antigenic determinants by searching protein sequences for the area of greatest local hydrophilicity. Hopp and Woods, 1981, make two assumptions in using hydrophilicity to find antigenic determinants: 1) antigenic…
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…
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…
Add ungapped sequences to a project
Sequences » Add ungapped sequences to a project
To add standard (ungapped) sequences, or additional sequences, to an existing project: You can add standard DNA, RNA or protein sequences from a wide variety of file types, including SeqNinja .star files. (See Advantages of using SeqNinja files). *Note: To add only a…
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…
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…
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…
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…
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…
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 >…
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.…
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.…
Merge two existing alignments (“Profile alignment”)
Perform a Multiple Sequence 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.…
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.…
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…
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,…
Options screen
Features » Map features (copy features to another sequence) » Options screen
The Options screen is the second wizard screen of the Map Features dialog, and lets you specify mapping options. Mapping – Use the text boxes or sliders to specify percent cutoffs for: Minimum feature coverage, where: Minimum sequence…
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…
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…
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 B: Perform a Mauve alignment using modified parameters
Perform a Multiple Sequence 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…
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…
Mauve alignment options
Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Multiple sequence alignment methods and options » Mauve alignment options
The Mauve alignment algorithm is for genome level alignment of nucleotide sequences. To run a Mauve alignment, select two or more nucleotide sequences and choose Align > (Re)Align Using Mauve. If you wish to change method options, instead choose Align > Align with…
Perform a Gene Homology Alignment
Perform a Gene Homology Alignment
The ability to do gene homology alignments was added in Lasergene 17.6, released in early 2024. This method is for nucleotide sequences only and is set up using a simple wizard with five screens. With this method, you can perform a phylogenetic analysis of much larger…
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…
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…
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…
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…
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…
Match Bar track
Tracks » Match Bar track
To display the Match Bar track: The Match Bar track is used to show similarities and differences between the query and target sequences as calculated using the Blosum 62 substitution matrix. This track is available in the Pairwise view only after performing a pairwise…
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…
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…
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…
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…
Map features (copy features to another sequence)
Features » Map features (copy features to another sequence)
MegAlign Pro’s feature mapping lets you map a single annotation or all annotations from a source sequence to a target sequence. The sequences involved must have been previously aligned. During the process, you may optionally filter annotations so as to…