Month: April 2014
-
MacVector at the NIH Research Festival April 23 – 24
For all of our NIH users: We will be at booth # 314 at the NIH Research Festival that is Wed. – Thurs., April 23 – 24. Please stop by for a demo of our new release, MacVector 13, and some other freebies, including discounted Easter candy!
-
Accessing BAM files from an Assembly Project file
All assemblies are stored using the BAM file format. This is a binary file that stores each read and where and which consensus/contig/reference it is mapped against. It is a compressed version of the pure text SAM format. For some post assembly tasks it is necessary to do further processing on the BAM file. To…
-
de novo assembly with Velvet
Velvet is a short read aligner that works very well on a wide variety of reads. Velvet excels at de novo assembly of sequencing reads from second and newer generation sequencers. In our latest release, MacVector 13, we’ve added Velvet to Assembler. This joins the existing tools, Phrap for Sanger sequencing reads and Bowtie for…
-
Calculating the melting temperature of PCR primers
Calculating an accurate melting temperature of your oligos, your template and of the predicted product is important to set the cycling parameters of your PCR machine. The Tm calculations in MacVector were updated in MacVector 12.6 to use a more modern algorithm. MacVector has always used thermodynamic “nearest neighbor” calculations, but there were two changes…
-
Troubleshooting: Resetting MacVector’s preferences
MacVector generally just works. However, even the most well behaved of applications sometime have problems. If you have restarted the application and restarted your Mac then a good troubleshooting step to perform next is to reset your preferences. For Mountain Lion and earlier deleting the preferences meant opening up Finder, navigating to your ~/Library folder…