New features in the upcoming MacVector 12 release.

By Chris | Published: August 31, 2010

We’re hard at work with our MacVector 12 which will be out toward the end of the year. This is a little longer than our usual six months since MacVector 11.1 came out. However, this is a big release! There has been a rewrite of various interfaces with the aim of making them more accessible to new users and for making cloning and constructs easier. It is also focused on increasing the performance of all graphical aspects of the interface. For example the map view has been completely redesigned and rewritten. Graphical overviews are the easiest way to visualise your sequence and in MacVector 12 even very large sequences with a rich level of annotation can be visualised and navigated easily.

Here are some of the new features:

Virtual Cloning

MacVector is a great tool for designing and documenting cloning strategies and this release has many improvements to make it even better. Restriction mapping enzymes that cut only at a single site are represented in a different colour to enzymes that cut at multiple sites, so making choosing suitable enzymes much easier.  Once you have digested a fragment the active window will highlight compatible sites in the vector sequence. So at a glance you can see where you can ligate your insert (see screenshot below).

GrowlNotification.png

Need to introduce a new restriction site into your vector with site directed mutagenesis or other techniques?  With MacVector 12 you will also be able to visualise “one out” restriction sites – These are potential restriction sites on the sequence where a single mutation will introduce a new restriction enzyme recognition site.

Graphical Enhancements

Visualising a graphical map or overview of your gene is far easier than sending your eyes dizzy with megabases of raw sequence. However, there are times when you just need to get down to the sequence. With MacVector 12 you can do both in the same window!  With the “Zoom to Residue” feature you can show the graphical map at sequence level.  You may now show the complementary strand and also show 3/6 frame translations of the sequence.  CDS features are displayed as the translated amino acid sequence when at residue level, rather than the graphic symbol used to represent them. Primer features are represented as residues at residue level too. The exact cut site of restriction enzymes will be shown indicating overhanging and blunt ends.

MacVector11MapSequenceLevel.png

Navigating around a sequence in general is simpler, especially for plasmids or other circular sequences. You can use arrow keys to nudge/slide through a selected segment (and have any results update appropriately). There is also a new Overview panel. This tool shows an overview of the entire sequence and allows you to drag a viewing box to show what region to show in the main Map window. The overview will only show the sequence in its true topology. This means that even if you are representing a plasmid as a linear sequence, for example to zoom into the multiple cloning site of a vector for ligating a fragment, then the overview tool will always show a circular sequence, with the location of the main window indicated.

Circular Sequence Support

Selecting across circular origins has been a long standing limitation in MacVector. In previous versions only a few algorithms worked across the ends of a circular sequence and you could not select across the origin of a circular molecule. With MacVector 12 you can select across the ends, so you can design primers across the ends, replace a segment there, or easily create features that span the split point.

Sequence Editor changes

Although MacVector supports the creation of 100% Genbank compatible features on your sequence, sometimes you just need to highlight a particular section of the sequence you are working on.  MacVector 12 now supports representing regions of the sequence in upper and lower case, and also to represent regions with coloured text. This allows easy one click annotation, or marking, of non-biological features.

Miscellaneous Changes

As usual there are a large number of minor improvements, as well as a whole stack of bug fixes. These include support for a new auto-single static license for large Network sites. In our ongoing aim to make MacVector the easiest to use application for sequence analysis many tool dialogs have been rewritten to be easier to use. The Symbol Editor has been rewritten.  The Graphics Palette has been completely redesigned to make it far easier to manipulate the map view to show your sequence how you want to see it.The Symbol editor has been redesigned to be easier to use and now has new symbol types – e.g. Full height rectangles, plain horizontal lines, plain lines with short vertical ends, single arrows with no drop to the sequence.  The Generate Transcript. dialog has been rewritten to make creating an RNA transcript from your sequence easier and much more.

There has also been continued work on the various graphic result windows to integrate them with the main Map tab. That will make it easier to convert results (e.g. open reading frames from the Nucleic Acid Toolbox) into features associated with a sequence.

Watch our blog for updates, and also subscribe to our RSS feed for the latest news.

MacVector 12 will be released towards the end of 2010.

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Keeping your copy of MacVector up to date

By Chris | Published: August 29, 2010

Following our regular releases, which are every six months or so, we regularly release minor updates. These updates generally contain important bug fixes. So it is always important to ensure that you are using the most updated version of a major version.

The latest updates for the last three major releases are:

MacVector 11.1.2

MacVector 11.0.4

MacVector 10.6.0

(please note that MacVector 10.6 is an update for all MacVector 10.5 and above users).

Incidentally whereas our policy for major releases is intensive testing with minor updates we prefer to get these out to users very quickly.

The easiest way to keep up to date is via the online notifier:

OnlineNotifier.png

(note the screenshot shows a development build of MacVector 12 that’s out soon!)

This will appear periodically whenever there is a new release. However, you can manually check by navigating to MACVECTOR PREFERENCES > SOFTWARE UPDATE and clicking CHECK NOW.

However, there are other ways to stay up to date. There’s the MacVector forums where as well as discussion we will post details of new releases. You can also subscribe to our RSS feed to be kept updated on all MacVector news.

..and of course there’s this very blog where we publish will generally publish whenever there’s a new release.

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MacVector 11.1.2 just released

By Chris | Published: July 28, 2010

We’ve just released MacVector 11.1.2, which is a minor bug fix release.

The bug fix list includes

  • Translations now correctly honor the genetic code shown in that dialog rather than the global genetic code.
  • You can now suppress the automatic re-ordering of reads in the Align to Reference window by holding down the <option> key when clicking on the OK button in the align dialog.
  • Trace files now print correctly.
  • BLAST matches to the complementary strand are now correctly numbered in the alignment text output window.
  • Restored the ability to read GeneWorks files.
  • Fixed an occasional crashing bus in the graphics display when editing a feature when the corresponding automatic Restriction Enzyme file was also open.
  • A bug where switching between Advanced tabs in the Primer3 dialog and editing one of the numeric fields would cause a crash has been fixed.
  • The annotated sequence text output now strips “/note=” from the front of any feature description text. This means that only the actual text you type into the Feature Editor Free-Form tab will now be displayed as the label for the feature.
  • MacVector can now open files saved from previous versions that had truncated LOCUS lines.
  • The ability to use non-ASCII Mac-Roman characters (e.g. ∆, ® and ©) in Feature descriptions has been restored.
  • Printing annotated sequences from the Editor tab now displays the correct translations.
  • Cross_match now takes quality values into account when evaluating the most likely insert segment in a Read.

Current users can download this here.  It will recognise your existing license.

 

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Graphics In MacVector: Exporting publication quality graphics.

By Chris | Published: July 20, 2010

This article is the first in a series of “howtos” resulting from the 2010 survey results.

It may not be at the cutting edge of sequence analysis but sooner or later most users of such apps are going to have to produce a graphic of their work, whether that is a plasmid map, a tree, an alignment etc..  There’s a world of difference between producing a rough and ready map of a construct for your labbook and producing a publication quality map for a publication. MacVector tries to make producing both as painless as possible. Most of the graphics within MacVector (including the Map view) use the Apple graphics library called Quartz. Quartz uses PDF technology to display graphics (reminiscent of NextStep and DisplayPostscript which was the predecessor to OS X!). It easily allows graphics to be exported directly in PDF format.  More importantly since most modern OS X applications also support PDF format, data can be exchanged via the clipboard using simple copy and paste procedures.  So exporting a plasmid map from MacVector can be as easy as clicking EDIT > COPY in the Map View, moving to the desired application (e.g. Microsoft Powerpoint) and clicking EDIT > PASTE. However, although easy it is important to understand that using copy/paste does not limit the quality in anyway. When you copy and paste from MacVector you are copying as a PDF, rather than the information that is on the screen. PDF is a vector format, as opposed to being a raster format, and can be enlarged to almost any degree without any loss of quality.  Furthermore when you paste into an application that supports this format, such as Adobe Illustrator, then you can directly edit the plasmid map in that applications.

In real terms this means that plasmid maps copied in this way can be resized without any loss of quality and without those jaggy lines.  Fonts will remain crisp as well regardless of what size they are displayed at. Whilst at the booth at the ASM2010 recently we thought it was a great example of how good the graphics could be by showing the metre high plasmid map and other graphics on the booth behind us. These were taken directly from MacVector.  As a smaller example the map below was also copy and pasted directly from MacVector.

http://macvector.com/blog/wp-content/uploads/2010/07/PastedMap.jpg

Using PDF in this way is the Apple recommended way of dealing with graphics, and it is supported by all the professional applications, such as Adobe Illustrator, Photoshop etc.

In addition the FILE > EXPORT menu will allow you to directly save the MAP view to a PDF file, and if you require a format other than PDF, then you can save a plasmid map in any OS X supported graphics format by utilising PREVIEW. This is an often underlooked utility found in the Applications folder on all Macs. It’s an incredibly useful tool for graphical data as it supports so many formats.

– Open MacVector on the MAP view, and select EDIT > COPY
– Open PREVIEW and select FILE > NEW FROM CLIPBOARD.

Once you’ve done this you can save the file as a PNG, JPG or any supported file.

If you need to obtain a exported image with a specific DPI (e.g. for a paper) then the easiest way is:

– Open MacVector at the MAP view, and select EDIT > COPY
– Open PREVIEW and select FILE > NEW FROM CLIPBOARD.
– Resize the map to the size you require.
– Open FILE – SAVE AS.
– Change the file type to TIFF, and change the DPI to the required value.
– Save the file.

In the next post we’ll discuss how to customise the actual graphics.

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Post-survey feedback!

By Chris | Published: June 27, 2010

We’ve just finished going through the survey results.  We’re very pleased with the amount and quality of feedback that you gave us.  There’s some excellent ideas in there, that you’ll start seeing with the next release (MacVector 12 is out later this year).  So once again thanks a lot to all who spent time to submit the survey. Of course as well as all of you receiving our gratitude one of you, Dr. Timothy Holton at the University of Queensland, will receive an iPad. We hope he likes it! We like ours.

Over the past few releases we have really tried to make MacVector easier to use (designing primers in as little as three mouse clicks, checking a sequenced construct in four, etc.),there were quite a few feature requests for functions that MacVector already does.  So it seems that we still have some work to do to make these functions easier to use! In the meantime the next few blog posts will address these points and show a few short tutorials.  The first will be on how easy it is to create publication quality graphics from MacVector.

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ASM2010

By Chris | Published: June 10, 2010

We had a great time at the ASM2010 in San Diego this year. San Diego is a great town, and even better with a bunch of scientists gathering in the bars and restaurants! Many great people stopped by the booth. Both old MacVector users, new ones, and people just interested in our software. Some of the more interesting things that we chatted about include how people are using the increasing availability and price of short read sequencing to “brute force” their analysis. However, with the relatively short bacterial genome (it was a microbiologist’s conference!) the problem is too much coverage! So we’ve already started discussing what we can do, so expect more short read assembly tweaks.

It was also very interesting to see that this was the year that Twitter really came of age as a useful tool for immediate communications!  Want to hear what’s the hot new poster being shown, which room is buzzing with a talk, then if you followed the #asmgm hashtag you quickly found out.  The only glitch being that a few early tweets used the #asm2010 hashtag (including us, ooops!). It was nice to see @comprendia and @jimhu at the booth.  Some other notable tweeters at the ASM were @phylogenomics, @Microbeworld. Here’s a tagcloud of the tweets during the conference.  Although we’ve only just, relatively speaking, started a MacVector twitter account, a few of us have been using Twitter for quite a few years now and it’s really great to see a useful, dare I say geeky, communication tool become mainstream at such an event (and a science one at that!).

A few people also completed our online survey at the booth, which is now closed, A lucky researcher at the University of Queensland will be receiving an iPad, and everybody who took the time to send us feedback will receive our gratitude.  We’ve had an unprecedented level of response from this survey. It seems that all of you want to run MacVector on Windows.  We also had a great number of feature suggestions, which we’re ploughing through now. As ever these will start to appear in the next few releases.

At this point we should show you a few nice piccies of how the booth looked, but we goofed and forgot to take any!  Actually there was so many visitors to the booth that we hardly had time to grab a coffee or even attend any talks, of which there were some interesting ones.  All in all an enjoyable conference.

We look forward to seeing you in New Orleans next year.

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MacVector at ASM 2010

By Chris | Published: May 15, 2010

The MacVector team will be attending the ASM 2010 meeting in San Diego.  If you are attending then please do drop by booth 240 (near the laptop lounge) to say hello!  If you are an user, then please do come and tell us what you think. Even if you think it is perfect (come top think of it, especially if you think it’s perfect!). If there’s something that MacVector does not do now that you really do want it to do then let us know.  At last year’s show the two main requests were support of next generation sequencing data and a Windows port.  The first was done last year with MacVector 11 and the latter is in progress.  It’s not just marketing blurb when we say we listen to our users!

We’ll be running impromptu demo sessions, and allowing you to play with MacVector and Assembler on a few Macs on the booth. As we did last year we’ll be handing out MacVector mousepads and other freebies. There will also be some 21 day demo CDs to take away.  You’ll also be able to take part in our survey (either online or on paper!) with a chance to win an iPad.

We’ll try to post some photos via Twitter.  If you also tweet, then please do follow us and say hello!  If you do so and you’re at the show we’ll give you a 10% “show discount if you want to upgrade your license, or buy a new one, or just ask at the booth and we’ll give you a discount as well.

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Flying for business is so 20th century!

By Chris | Published: April 23, 2010

The volcanic ash cloud covering most of Europe is a timely reminder of just how powerful nature is. With the disruption to air travel it’s also a great reminder of just how most communications can be done without meeting face to face. Whereas it is always nice to meet with MacVector users, any such visit inevitably involves substantial travel. With the tools available now, there’s almost no need to travel. We’d prefer to keep our travel costs down (& our software!) and the cost to the environment. We’re also sure you’d prefer to be in the lab, rather than being sat in a meeting!

Here at MacVector, Inc. we use many different communication means, both to keep in contact with each other and to communicate with MacVector users. For internal chat we use Skype and iChat/Mobile me. For voice conferencing we mainly use Skype again and also our own phones which are also running on voip. We’ve also used iChat for video conferencing. When it works it is brilliant. However, it is quite temperamental. Skype is slower but more reliable. For file sharing we use the incredible Dropbox. Is there an easier way to share documents and files with colleagues? For mobile communications we have a mixture of devices, there’s iPhones, iPads, Android phones, and others.. We’ve used a variety of webcasting platforms. However, unfortunately Mac seems to be a second class citizen in this world. Our current favourite (for quite a while now) is Adobe Connect Pro. The voice function is far from perfect, but the video performance for sharing a screen is very good. Far better than every other platform we have tried.

Finally we have our twitter feed, our RSS feed, our forums, our website and of course this very blog you are reading.

However, it is nice to get out of the office and meet MacVector users for real! We will be visiting the ASM in May. If you’re also attending please do pop along to see us. Pick up a MacVector mousemat whilst you are there, and you’ll also have a final chance to win an iPad with our survey.

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Hidden labels in MacVector 11.1?

By Chris | Published: April 19, 2010

We made a whole slew of graphical enhancements to MacVector 11.1. Most of these were intended to increase the performance for viewing the graphical map of very large sequences.

One of these hides the labels of features when you are showing a heavily annotated sequence. However, in hindsight we set the default value for this to be too low! We’ll change this for the next release but if this annoys you, then change the default to be 1000 instead. To do so go to the MacVector Preferences and change the value in the Map View preference pane.

Primer3_Capture2.jpg

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Short read improvements to MacVector 11.1

By Chris | Published: March 15, 2010

The ability to produce de novo assemblies of short read data was introduced into MacVector & Assembler 11 and we’ve enhanced this in MacVector 11.1. Now Assembler stores and visualises metadata on the type of short read you have and also stores and deals with the quality data stored in a better way.

Mixing your reads

Currently there are three major types of short read data about, due to the fact that there are mainly three next generation sequencers producing considerably different read lengths.

– Illumina reads which are generally 66bp in length (the first generation of Solexa sequencers produced reads of 33bp long).

– 454 reads which can be 400 to 500 bp long

– SOLiD reads which are around 50bp long.

It is important to know which sequencer your reads have come from as length is not the only specific characteristic they possess. So with MacVector 11.1 we have introduced new feature types to indicate which types of read it is. So whether you mix Sanger, with 454, and a dash of Illumina reads, your assembly project will always keep the source of the reads stored in the metadata of the project. Furthermore the default symbol for each read type is different, and can be easily visualised.

http://macvector.com/blog/wp-content/uploads/2010/02/ShortReadFeatureType.png

Yet another sequence file format inconsistency!

An unfortunate fact about file formats in the bioinformatics world is that there are just so many of them! Most of them giving a slightly different approach to the same question. So it is nice that the Fastq format seems to be already fairly ubiquitous amongst raw data storage for short read data. Which is the main reason that we chose it to support short read data in MacVector. However, on the downside already there are three variations in the way that quality scores are stored in the format (actually there are variations in the sequence labels as well, but let’s just consider the quality scores). As well as the basecalled sequence, the Fastq format stores quality data encoded as a single character using the ASCII code for that character representing the value. All three variations of the format use that strategy. However, the actual number stored and the way it is encoded into the ASCII character does vary. The first generation of Illumina machines (when the company was still called Solexa) used a proprietary quality code. The current generation of their sequencers use the more recognised Phrap quality scores. However, they do store this number differently to the more recognised “Sanger” format which stores a Phrap quality score with a range of 0 – 93 using ASCII codes of 33 to 126. It is very important to distinguish when data is in the old Solexa scores. It is less important to distinguish between the later Illumina format, as reads will only be relevant when scores are very high and such high Phrap scores are unlikely.

So as well as distinguishing which sequencer produced the data, Assembler now also support the import of Fastq reads in all three types of quality data, and will take this into account when being assembled.

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