Category Archives: Tips

MacVectorTip: quality score visualization in sequence assemblies.

Quality scoring of Assemblies and Align to Reference alignments can be visualized directly on the sequence. Residues can be shaded according to their quality scores. These can be displayed anywhere quality values are available, including de novo and reference assemblies in Assembler and Align to Reference alignments. A Shading toolbar button lets you turn on […]

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MacVectorTip: Assembling Fungal Genomes using SPAdes

MacVector with Assembler can assemble bacterial genomes in just minutes on quite modest hardware. Currently MacVector has four de novo assembly tools (SPAdes, Velvet, Flye and Phrap). But what of larger genomes? It is currently impractical to run de novo assemblies of Human genomes on a low cost Mac, though RNA-Seq analyses against the human […]

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MacVectorTip: Viewing external database entries for features in a sequence.

Sequences, or regions of sequences, can be linked to external databases. For example an entire sequence entry or for when annotation tools are used to annotate proteins with domain or motif information (for example InterProScan). Very useful for when you want to view more detailed or updated information. Within the Genbank specification, which MacVector extensively […]

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MacVectorTip: How to Customize Window Button Toolbars

Like many Mac applications, MacVector takes full advantage of the built-in ability to add, delete and rearrange the action buttons on window toolbars. To make these changes, right-click (or [ctrl]-click) in the gray space on any toolbar and a context-sensitive menu will appear. Choose Customize Toolbar and a dialog will be displayed with all of […]

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MacVectorTip: Understanding Color Groups

You can align hundreds, or even thousands of protein sequences within MacVector using three different alignment algorithms – ClustalW, MUSCLE or T-Coffee. Once aligned, you may be familiar with the colorful display in the Editor tab. But there’s more to this than pretty colors. The default Color Group in MacVector is one called “Chemical Type”. […]

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Weekly Tip: Use Hash Value = 12 for speedy genome comparisons with Create Dot Plot

MacVector’s Analyze | Create Dot Plot function can be used to compare entire genomes very quickly to get both an overall view of similarity (large inversions and duplications) while providing the ability to “drill down” to the residue level to see individual SNPs. One of the keys to ensuring the calculations complete in a reasonable […]

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MacVector’s Primer Database – Importing primers from Excel

Many molecular biologists keep lists of their primer sequences in Excel or some other spreadsheet tool. Previously MacVector had a separate utility that allows you to import primers kept in spreadsheet format into a Primer Database for direct use within MacVector. With the release of MacVector 18.2 we have integrated this functionality within MacVector. Rather […]

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MacVectorTip: Scan For… Missing Primers: Automatically display Primer Binding Site on your sequences

MacVector’s Scan DNA For.. tool allows you to automatically display restriction enzyme recognition sites, putative ORFs, CRISPR PAM sites, missing annotation and also it will display primer binding sites from your own Primer Database in each DNA sequence that you open. Here’s an example of a couple of primers displayed on the pET 47b LIC […]

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MacVectorTip: Using the Align to Reference Shading and Trimming toolbar buttons

MacVector’s Align to Reference Editor and the Contig Editor in Assembly Projects have two useful functions for visualizing assemblies. The Shading button turns on background coloring of the residues in the upper pane, based on quality values (these can be from Sanger reads or from NGS reads). The scale ranges from a dark red for […]

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MacVector Tip: a complex subsequence pattern example.

MacVector’s Subsequence tools allows you to search for motifs in both protein and DNA sequences. As well as a library of existing subsequence files, such as promotors and transcription factor binding sites, you can keep a library of your own subsequence matches. Subsequences libraries are multiple patterns kept in a single file. A search will […]

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