General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Category Archives: Techniques

Howtos, tips and descriptions of various techniques for using MacVector.

Importing features from a Genome Browser

By Chris | Published: May 14, 2012

One of the new features in MacVector 12.6 is the ability to annotate sequences based on the features stored in GFF/BED/GFT files that many Genome Browsers will export data as. MacVector 12.6 will annotate an empty or annotated sequence with the features stored within these files. BED, GFF, GTF, and GFF3 formats GFF, GTF, GFF3 [...]

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MacVector 12.5: Creating alignments with T-Coffee and Muscle

By Chris | Published: January 8, 2012

With MacVector 12.5 we’ve added additional multiple sequence alignment (MSA) algorithms. Muscle and T-coffee have been added to the Multiple Sequence Alignment editor complementing the existing ClustalW algorithm. We’ve wanted both of these for a while now and judging from the results of last year’s survey so have many users. Both T-Coffee and Muscle are [...]

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MacVector 12.5: Sequence Assembly made easy.

By Chris | Published: October 24, 2011

This is part of a series of posts about and leading up to the release of MacVector 12.5. Assembler has always made it easy to assemble your sequencing projects. It hides the complicated algorithms and provides a point and click interface to show you the results. With the release of MacVector 12.5 the range of [...]

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Label customisation using metatags in the Map View

By Chris | Published: April 12, 2011

MacVector has always given the user great control in being able to customise the map’s appearance. By default the label will show the full text description of a feature and all its qualifiers (see the first metatag in the list below). However, the label can contain whatever text you want it to display. Obviously you [...]

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Aligning primers against a template sequence

By Chris | Published: November 4, 2010

A common request, especially in our recent survey, is to align existing primer sequences against a template sequence. There are many ways to do this in MacVector, depending on what your requirements are Using the Find dialog For quickly finding a single primer in a sequence the Find dialog is the first point of call. [...]

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Clustering an alignment

By Chris | Published: October 25, 2010

Sometimes it is useful to sort, or cluster, an alignment according to the similarity/identity of its sequences. With such a sorted alignment you are able to more easily visualise closely related sequences as they will be together in an alignment with more distantly related sequences being much further apart. If you want to quickly cluster [...]

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Creating your own subsequence library of primers

By Chris | Published: October 15, 2010

As mentioned in a recent post MacVector has a powerful feature called Subsequence searches. This function allows you to keep a library of sequence pattern matches, using a powerful nomenclature with up to three parts, and quickly scan protein and nucleic acid sequences with this library. .Although MacVector ships with a number of collections of [...]

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Jaspar, MacVector & Subsequence searches

By Chris | Published: October 10, 2010

MacVector allows you to find motifs, primers, transcription factor binding sites, or any significant region with a consensus sequence, in your sequence using a powerful feature called subsequence searches. This function allows you to keep a library of sequence patterns of either nucleic acid or proteins. You can use subsequences with complex patterns for the search [...]

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Displaying translations alongside your DNA sequence

By Chris | Published: September 24, 2010

There’s a few ways to display an amino acid translation in the same window as your DNA or RNA sequence. (1) You can show either three or six frame translations directly in the editor. To do so simply press and hold down the STRANDS toolbar button. You’ll see the following menu and be able to [...]

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Graphics In MacVector: Exporting publication quality graphics.

By Chris | Published: July 20, 2010

This article is the first in a series of “howtos” resulting from the 2010 survey results. It may not be at the cutting edge of sequence analysis but sooner or later most users of such apps are going to have to produce a graphic of their work, whether that is a plasmid map, a tree, [...]

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