Search - User Guide to MegAlign Pro

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,…

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

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…

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…

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…

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 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…