KeyServer 7.0 was released a few months back. There is no need to upgrade your license server for MacVector. However, if you do want to upgrade then you must download the latest installer direct from Sassafras. This version (7.0.0.3) contains important bug fixes and is a later version than the KeyServer installer on the MacVector 12.5 CD.
You will also need to contact MacVector Support to request a new network license.
Sometimes when a subsequence file, that has been created by an version of MacVector prior to MacVector 11, has been stored on a remote filesystem or has been emailed MacVector will refuse to open the file.
Mac files are generally comprised of two pieces: A data fork and the resource fork. Prior to the release of OS X Leopard (and OS9 and earlier) used two pieces of information called TYPE and CREATOR to specify which application would be used to open a document. This information was stored within the resource fork. The resource fork has been lost from the file during the transfer, or more accurately due to it being stored on a non-HFS filesystem which only recognises the data fork.
With older versions of MacVector this would have required the resource fork to be recreated and a new TYPE/CREATOR information to be specified and stored within the new resource fork. However, one of the many major changes made to OS X as been the move from the traditional way of opening files using the resource forks TYPE/CREATOR information stored within the resource fork to the use of Universal Type Identifiers (UTI) and file extensions. MacVector now registers many file extensions with OS X when installed. For example “.nucl” is a single NA sequence and “.renz” is a restriction enzyme file. NA subsequence files have the “nsub” extension. If a file is missing the resource fork then OS X will rely on the file having an extension on whether it can open it or not.
So fixing your subsequence files is as easy as literally adding the “nsub” file extension to your file.
Do remember though that MacVector will always try its hardest to recognise a file’s format. So even if double clicking on a file will not open it (it’s the operating system that’s at fault here, not MacVector) then using FILE > OPEN from within MacVector will generally work. Saving that file will then recreate the resource fork AND add the extension.
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If you are a user of MacVector or have any interest in sequence analysis for molecular biologists then you may be interested to know that there’s a workshop about MacVector at the University of Pennsylvania this Thursday open to faculty, students and researchers.
When: Thursday February 9th 9:30 to 11:00 Where: Blockley Hall, Room 1311
“Dr Kevin Kendall will present an informal 90 minute workshop for both beginners and long-time users of MacVector.The workshop will review how to use the basic functions and features in MacVector, as well as covering more advanced workflows and new functionality in the latest releases, MacVector 12.0 and 12.5. He will be happy to answer any questions about MacVector that you may have, as well as previewing the functionality planned for MacVector 12.6.”
Light refreshments will be provided.
Please register for the workshop on the University Bioinformatics Group website
Technorati Tags: MacVector
If you are a user of MacVector or have any interest in sequence analysis for molecular biologists then you may be interested to know that there’s a workshop about MacVector at MSKCC this Wednesday open to MSKCC faculty, students and researchers.
When: Wednesday February 8 from 11:00 to 12:30 Where: Room RRL B20
“Dr Kevin Kendall will present an informal 90 minute workshop for both beginners and long-time users of MacVector.The workshop will review how to use the basic functions and features in MacVector, as well as covering more advanced workflows and new functionality in the latest releases, MacVector 12.0 and 12.5. He will be happy to answer any questions about MacVector that you may have, as well as previewing the functionality planned for MacVector 12.6.”
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If you are a user of MacVector or have any interest in sequence analysis for molecular biologists then you may be interested to know that there’s two workshops about MacVector at The Rockefeller University this Tuesday open to all Rockefeller faculty, students and researchers.
When: Tuesday. Feb. 7, 2012 at 10:00 - 11:30 and 1:00 - 2:30 Where: Rockefeller, Weiss 302
“Dr Kevin Kendall will present two informal 90 minute workshop for both beginners and long-time users of MacVector.The workshop will review how to use the basic functions and features in MacVector, as well as covering more advanced workflows and new functionality in the latest releases, MacVector 12.0 and 12.5. He will be happy to answer any questions about MacVector that you may have, as well as previewing the functionality planned for MacVector 12.6.”
Light refreshments will be provided.
Please register for the workshop.
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Only MacVector 9.5 and later versions will run on OS X 7 Lion.
Apple started transitioning their processor architecture from PowerPC (PPC) to Intel’s x86 in 2006. The Macbook Pro and the iMac being the first Intel Macs. When they did so they gave Xcode (the OSX development environment) the ability to create Universal Binary application. These contain native executables for both PPC and x86 CPUs. So giving these applications the ability to run natively on both types of Mac.
However, to support earlier applications that had only been available as PPC executables they included a PPC Emulator called Rosetta (named after the Rosetta Stone). This allowed PPC only applications to run on Intel x86 Macs.
OS X 10.5 Leopard was the last release of OS X that was distributed as a Universal Binary OS. With OS X 10.6 Snow Leopard being a x86 only release. That is it will not run on PPC Macs. Even so they kept Rosetta as an optional install (previously it was installed by default). However, OS X 10.7 Lion does not include Rosetta and you cannot install earlier versions. This means that PPC applications will no longer run on Lion. In reality this is only applications that are over six years old.
MacVector 9.5 (released in 2006) was the first Universal Binary version of MacVector. Previous versions are PPC only and will not run on Lion.
If you are running such an old version of MacVector then your options are limited to either upgrading MacVector or not upgrading to Lion. You can still upgrade such an old version of MacVector at a significant discount. Contact Sales to request a quote or visit the website. There’s many other reasons to upgrade as well. The interface has changed substantially since MacVector 9.5 being more powerful and easier to use. There’s also many new tools with enhancements to older ones. The latest release is MacVector 12.5 and this release has improvements to sequence assembly (support for NGS reference assemblies using Bowtie) and extra options for multiple sequence alignment with Muscle and T-Coffee added.
Technorati Tags: apple, lion, OSX, Universal Binary
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 progressive alignment algorithms as is ClustalW. Progressive alignments generally build a guide tree that represents the pairwise relationships between each possible pair of sequences in the alignment. A multiple sequence alignment is then built sequentially using the tree as a construction guide. T-Coffee builds a library of all pairwise alignments but also aligns each sequence in the pair with a third sequence in the sequence set before building the MSA. Muscle does not do a pairwise alignment but instead uses an approximate method of comparing the number of short subsequences (k-mers, k-tuples or words) that each pair of sequences share. You can immediately see how this is much faster for alignments containing many sequences where the number of pairwise alignments needed to construct the tree is high.
T-Coffee is regarded as being slightly slower than ClustalW but will produce more accurate alignments for distantly related amino acid sequences. Here’s the original publication. Incidentally T-Coffee stands for Tree based Consistency Objective Function For AlignmEnt Evaluation.
Muscle is generally regarded as faster than Clustalw and T-Coffee at the penalty of being slightly less accurate.
All three algorithms are integrated into the MSA editor. This means you can try all three algorithms on the same alignment to see the results.
Here’s a few benchmark for protein sequence alignments (the files are in the Sample Files folder in the MacVector application folder:
– Clustalw: 1min26secs
– Muscle: 12 seconds
– T-Coffee: 17mins22secs
Because of the initial step of constructing the pairwise alignments tree, progressive alignment algorithms have difficulties with alignments where all sequences do not share a common region. For example take an alignment of three sequences where you have 5kb sequence and two regions of this sequence of around 1KB long. One subsequence aligns from 1,000 to 2,000 of the 10kb sequence and the other aligns at 4,000 to 5,000. Most progressive alignments will try to create initial pairwise alignments of all combinations of sequences and that skews the alignment so that it prefers to align the sequences so that there is at least one segment of overlap between all of the input sequence. Due to not creating pairwise alignments the “Muscle” algorithm is unique amongst these three algorithms as it will align this type of data as long as the “Diagonals” optimization parameter is set to “On”.
Technorati Tags: Sequence Alignments, MacVector
With the release of OS X 10.7 Lion Apple made significant changes to the structure and permissions of various important folders. For example the Library folder in the user’s home folder is now hidden.
A consequence of this is that on Lion (and all versions after that) older versions of MacVector do not have the correct permissions to create the required MacVector License folder (Snow Leopard and earlier are fine). Note that only MacVector 9.5 and later will run on Lion. Much older versions will not run.
With the release of Mavericks this situation changed further. You must be running MacVector 10.5 or later. You cannot activate a license with MacVector 10.0. For Mavericks all versions before MacVector 13 are affected.
The following error is seen:
Unable to write the license details to disk. Please contact MacVector Support. [CODE=-5000]
The following steps should fix it:
“[StartupHD]/Library/Applications Support/ MacVector
[StartupHD] refers to whatever name you call your hard drive.)
“[StartupHD]/Library/Applications Support/ MacVector
Now try reactivating the license.
If this does not work then please contact Support@macvector.com.
Getting back to the lab after the end of the year break is always a shock! You’ve might have been popping into the lab over the vacation to maintain your experiments, but now you need to get those experiments moving again and start getting the results in.
So after you’ve chatted about the holidays with your colleagues have a slow start to 2012 and take the opportunity to keep your copy of MacVector up to date. MacVector 12.5 was released at the end of last year. So if you’ve not yet done so then do so here! It’s also a good idea to run a few system maintenance tasks to make sure your Mac is running great.
Happy New Year!
At the end of 2011 we’d like to say thank you for your business and continued trust in us. MacVector, Inc. is about to celebrate its 5 year anniversary and it remains our mission to keep MacVector the number one sequence analysis application for the Mac. We try to listen to our customers and react quickly to the needs and trends in the Molecular Biology world and add the features most requested. We have released eight major versions in that time and many minor versions.
We have a lot to look forward to in 2012. MacVector 12.6 will be released in the first quarter of 2012 with some great new primer design tools. We’ve also got another release planned for the backend of the year.
But for now, we thank you and we wish you a prosperous, happy and enjoyable New Year from the whole MacVector team.
But before we all break for the end of the year remember that we’ve just released MacVector 12.5. You’ve probably seen the release via Software Update inside MacVector but if not you can download it from our website if your license is valid for this release or download a 21 day trial.
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