MacVectorTip: How to Toggle Between Single-Letter and Three-Letter Amino Acid Translation Code

Many views in MacVector display amino acid translations above or below DNA sequences. Typically, these are from CDS features, but can also be the 3/6 frame translation of a sequence. You can display the amino acids as either the single-letter code, or as the three-letter code. You can toggle the setting using the MacVector | Preferences -> […]

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MacVectorTip: Viewing genotype changes in Align to Reference assemblies

The latest releases of MacVector, MacVector 18.0.1 (Intel) and MacVector 18.1.1 (Intel and Apple Silicon) have some tweaks to the output of the SNPs tab in the Align to Reference assembly window. The genotypes of any SNP changes now follow a consistent standard, and short deletions are also reported. If the region containing the nucleotide […]

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Make more of your alignments with MacVector 17.5

Our latest release MacVector 17.5 gives you new tools to make the most of your alignments. It displays shared domains in protein alignments to visualize the relationships between aligned proteins. It introduces Flye for de novo assembly of PacBio and Oxford Nanopore long reads and a slew of enhancements to the Contig and Align to […]

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Use the BLAST Map to better identify blast hits

With the advent of cheap Next Generation Sequencing technologies, there has been an explosion of whole genome sequences deposited in BLAST databases. One consequence of this is that, particularly for sequences of bacterial origin, most of the significant hits are to entire genomes. The classic BLAST results show the sequence alignments, but give no indication […]

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Confirming a small sequencing project against a reference sequence

Align to reference is a perfect tool for mapping small sequencing projects against a reference sequence. It’s perfect for accurately and quickly: – Confirming the sequence of a cloned fragment – Sequencing across the ends of a cloned fragment to confirm the junction sequence – Screening clones from a site-specific mutagenesis experiment to identify successful […]

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How to save contig consensus sequences from assembly projects

The MacVector Assembler module lets you create projects, populate them with Sanger Sequencing or NGS data files (or any sequences in a format that MacVector can read) and then assemble them using the popular phrap and/or Velvet assemblers. Typically, the result will be a collection of contigs that you might want to use in additional […]

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How to align DNA sequences based on their amino acid translations

A new tool in MacVector 15 allows you to align DNA sequences based on their amino acid translated sequence. For most alignments in MacVector you will use the Multiple Sequence Alignment tool. This allows you to align DNA or protein sequences using either Muscle, Clustalw or T-Coffee. MacVector 15 now allows you to align DNA […]

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Tweak your DNA Matrix for better Align To Folder searches with primers

You can use the Database | Align To Folder function as your own “personal BLAST search”, comparing a sequence to all of the sequences in a target folder hierarchy. The files in the folder can be in any format MacVector recognizes, including fasta and fastq formatted multiple sequence files. Many users take this approach to […]

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Know Your Alignments

We often get asked “how do I do an alignment” using MacVector? Well, the answer to that is always “it depends”, and it depends on what you want to learn about your sequence(s). Here’s a quick summary of the different types of alignments and what you would use them for: Multiple Sequence Alignment (File | […]

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Changing the sequence alignment match and mismatch characters

Many MacVector analysis functions (e.g. Align To Folder, Create Dotplot and Internet Blast Search) display alignments where there is (by default) a vertical “|” character indicating a match between the query and database sequences. While this is very useful for identifying matching residues, sometimes you might be more interested in those residues that do NOT […]

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