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Author: Chris

  • MacVector Talk: July 2014: Sequence assembly on the desktop with MacVector and Assembler.

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    Generating sequencing data is cheaper than it has ever been. However, with this increase in data has come a problem with easy analysis. Assembling 20 reads for your site directed mutagenesis project is easy. Why should dealing with 20 million reads of your bacterial genome be any harder? In our Summer newsletter we talk about…

  • Using Applescript to batch convert files.

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    Up until MacVector 13 Applescript support was fairly limited. However, with this release we’ve started to expand it. The first enhancement has been to improve the export of files. Now you can export files to any supported format. Over the next few releases this support will be further expanded to include some analysis tools. If…

  • MacVector at the ASM in Boston

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    We’ll be at the 114th American Society for Microbiology this coming Saturday, May 17-20, 2014 in Boston. Come visit us if you are also in Boston. We’re on booth 345. We’ll have demo CDs of our latest release, MacVector 13, and there’ll be mouse pads and incubator tube floaties to pick up. Probably candy too!…

  • MacVector 13.0.1 released.

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    We’ve just released a minor update, MacVector 13.0.1. This release has a few minor bug fixes that have been reported in the past month. However, this release also sees the introduction of online updating via Sparkle. This allows you to update your copy of MacVector in place. Once a day MacVector will check our website…

  • Accessing BAM files from an Assembly Project file

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    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

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    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

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    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

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    EDIT: December 7, 2018 Updated for macOS Mojave EDIT: August 26, 2014 The script now works for all versions of OS X. For versions before Mavericks the old preferences files are moved to the Desktop rather than being deleted. MacVector generally just works. However, even the most well behaved of applications sometime have problems. If…

  • Importing sequences from ENSEMBL

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    There’s a few different ways to import annotation from the ENSEMBL database browser, as well as other databases. Using Genbank The easiest way to export from ENSEMBL and keep all annotation is to use the Genbank format. The default format will be FASTA which has no annotation. With Genbank all the annotation is stored in…

  • Implementing a new activation code for network license users

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    When you’ve got a lot of licenses and a lot of computers to manage, a network license is the most effective way of letting your users access their favourite sequence analysis app for the Mac! MacVector network license use the KeyServer network license software from Sassafras. However, in addition to the KeyServer setup MacVector also…