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Accessing BAM files from an Assembly Project file
Read more: Accessing BAM files from an Assembly Project fileAll 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…
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de novo assembly with Velvet
Read more: de novo assembly with VelvetVelvet 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…
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Calculating the melting temperature of PCR primers
Read more: Calculating the melting temperature of PCR primersCalculating 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…
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Troubleshooting: Resetting MacVector’s preferences
Read more: Troubleshooting: Resetting MacVector’s preferencesEDIT: 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…
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Importing sequences from ENSEMBL
Read more: Importing sequences from ENSEMBLThere’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…
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Implementing a new activation code for network license users
Read more: Implementing a new activation code for network license usersWhen 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…
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Testing primers with MacVector 13
Read more: Testing primers with MacVector 13New to MacVector 13 is the ability to quickly test a pair of primers. Previously to test a pair of primers with the Primer3 tool you needed to modify the expected product and reduce the stringency of all parameters so that your primers would be accepted. Now when you enter a pair of primers into…
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MacVector 13’s redesigned results windows
Read more: MacVector 13’s redesigned results windowsBefore MacVector 13 all the results windows could sometimes get in the way. Some tools, such as the restriction enzyme tool, can generate up to six different results windows. Such as a list of all enzymes that cut a sequence, a list of all non-cutters, a restriction map, etc.. This is all useful information and…
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Public beta of MacVector 13
Read more: Public beta of MacVector 13There’s a public beta of our imminent release MacVector 13 ready for downloading and testing on our website. You just need an active license for MacVector 12.7 to run this. Watch out for the new easier way of installation (no installer, just drag to your Applications folder!). As well as a redesign of the interface…
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MacVector 13 is almost out…..!
Read more: MacVector 13 is almost out…..!The next version of MacVector is almost ready to be released. MacVector 13 is more powerful and intuitive than ever. There’s not only some very useful new tools and features but MacVector 13 has had a redesign. A fresh new interface MacVector 13 looks great. The interface is now muted to suit the look and…
