The classic algorithm for aligning multiple protein sequences is ClustalW. Normally, it does a great job of aligning related DNA and Protein sequences and can handle thousands of sequences if required. However, one place where it struggles is if you are aligning non-overlapping segments of DNA or Protein against a parental full-length sequence. The reason […]
By default, MacVector uses upper case letters for sequence residues. However, you can also use lower case characters if you wish. Changing the case of residues does not affect the MacVector analysis algorithms – GAATTC, gaattc and gAAttC are all considered valid EcoRI sites for example. If you want to set a short region of […]
While most features you might encounter in DNA files have a simple start and stop location on the sequence, some features are segmented. For example, the coding sequence of a protein encoding reading frame containing introns is represented by a segmented CDS feature on the genomic DNA. MacVector has always understood that the individual segments […]
So, you have a primer sequence and you want to know what its melting temperature is? Well, MacVector has a lot of Primer Design functionality, and sometimes its difficult to know where to start. If you have MacVector 12.6 or later, the easiest and quickest way to do this is using the Quicktest Primer functionality. […]
Following on from my last post about turning on translations in the sequence Editor, I thought I should point out how to display amino acid translations using the 3-letter code rather than the default single-letter code. I don’t know about you, but I have a hard time remembering that “W” is the single-letter IUPAC code […]
If you have used MacVector for many years, you’ll remember the days when the single sequence editor was THE main way you interacted with MacVector. When MacVector 10 was introduced back in 2007, the Editor became just one tab in the single sequence window along with Map, Features and Annotations tabs, all of which at […]
Some of the most common support calls we get are from users who are not sure how to use a particular feature in MacVector and would appreciate having someone walk through the steps with them. In many of these cases, it turns out that we have published tutorials that have exactly the information they are […]
Following on from the graphics tips of the last few posts, here’s one that can save you a lot of time if you are the sort that likes to keep the appearance of your features consistent between sequences (like me). Suppose you have downloaded a sequence from Entrez, or been sent a sequence in GenBank […]
MacVector’s Map graphics can provide highly detailed views of individual sequences in linear or circular format, or of the results of many analyses. You can print these to a printer with no loss of detail, even if blown up to many magnifications. However, it is often more useful to insert these graphics into other applications […]
The Map tab of MacVector’s single sequence editor displays highly detailed graphics showing sequence in circular or linear format. It is highly customizable and the graphics can be printed or copied to other applications using Apple’s internal PDF vector graphics format, resulting in images that can be scaled to any size with no loss of […]