General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Updated Gateway Restriction Enzyme file

By Chris | Published: August 15, 2011

Here’s an updated restriction enzyme file for Gateway cloning with MacVector.

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MacVector and upgrading to Lion.

By Chris | Published: August 12, 2011

The latest version of OS X, Lion, has been out for a few weeks and it’s a great operating system. MacVector 12 has been tested and although not yet officially supported, it works great..

Nonetheless even though we’ve not yet come across any issues we are committed to fixing bugs. So if you are running MacVector 12 and have already updated to Lion then please do not hesitate to email us or comment on this blog if you find a bug, even if it’s just a little niggle.

MV12onLion

If you are not running MacVector 12 then there are some issues. Lion does not include Rosetta and because of this if you are using MacVector 9.5 or earlier then this will definitely not work on Lion.

MacVector versions between 10, 10.5 and 10.6 may still work although these have not been tested yet. MacVector 11 and 11.1 appear to work although it is possible that there are issues.

So before you upgrade your Mac make sure you upgrade your copy of MacVector and discover why MacVector 12 is the best and easiest to use version of MacVector yet!

Why upgrade MacVector?

MacVector has always been designed to be the easiest sequence analysis application to use on the Mac. With the latest release MacVector’s strengths are:

- Graphics: displaying feature rich annotated sequences with a sequence overview allowing you to see your full sequence at a glance

- Subcloning: A point and click interface allows you to select RE sites, digest, then ligate into a vector with ease! Compatible sites are highlighted with a Klenow blunting tool if there are none. MacVector also supports Gateway and TOPO cloning.

- Comparing sequences: You can align cDNA/mRNA/EST clones against genomic sequences, Blast your sequence, search and align against multiple sequences on your hard drive, generate dot plots and much more. Assemble reads against a template sequence with easy SNP analysis.

- Open your data from many sources: direct from Entrez, from Vector NTI databases, from many sequence formats (e.g. GenBank, EMBL, GCG etc) or from sequencing facility files in Fastq, ABI or SCF formats.

- Sequence Annotation: A wide array of algorithms combined with the drag and drop of results to your sequence makes it a quick process to annotate your blank sequence with features. Auto annotation lets you quickly annotate new sequences based on your own collection of curated sequences.

- Designing primers: Click on a feature in your sequence, run the analysis and get a ranked graphical list of the best primer pairs to amplify that feature. You can also design internal hybridisation primers for realtime PCR analysis with additional functions to check/design sequencing primers.

- Sequence assembly: there are tools to easily create de novo assemblies in a few steps or simply compare your sequencing results against the template of your new construct.

The cheapest time yet to upgrade

If all those features are not enough then to help you upgrade we are offering a discount on all upgrades. Upgrade before the end of September and we’ll give you a 25% discount on even very old copies of MacVector. This means you can upgrade to MacVector 12 for as little as $450*

To upgrade request a quote and enter LionUpgrade in the promotional code box

Remember all upgrades of MacVector also include 12 months of free upgrades. This means upgrading now means that you will receive MacVector 12.5 which is due for release later this year.

….and as well!

If you are not convinced about upgrading your copy of MacVector then if you request a quote by the end of August we’ll send you a mousepad to help you remember that which codon stands for Aspartate…..

MousepadPhoto
FloatiePhotoCropped+Resized+rotated

…and when we receive your order we’ll add a floatie for your water baths!

 

 

 

*For upgrading MacVector 8.1 or higher in the US. Please contact sales@macvector.com for other pricing.

 

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Designing primers that do not bind at multiple places in your template

By Chris | Published: August 11, 2011

The default settings for Primer3 do not actually check for whether a primer will bind at multiple places in the template. To turn this on use the PRIMER vs PRODUCT setting in the PRIMER BINDING tab (the Primer3 parameter is “PRIMER_MAX_TEMPLATE_MISPRIMING”). The default value is -1, which means do not check. Change this to 1 to start checking, or increase the number to increase stringency.

This should now find any duplicate alignments.

Incidentally an upcoming release will have a special “QuickPrimer” tool for checking such issues as well as the Primer3 tool.

Primer3 Primer2Product

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MacVector, Assembler and network licensing.

By Chris | Published: August 8, 2011

We recently changed the way that Assembler network licenses are shared out to make it easier for many users to share a single license. Previously an Assembler license was checked out whenever you loaded MacVector with Assembler.  However, now an Assembler license is only checked out when you start a new assembly project or open an assembly project. Thus leaving it free for one of your fellow users if they need Assembler. This means that a license can now be shared a lot easier than before.

Contact MacVector Sales if you are interested in adding Assembler to your license

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MacVector on OS X 10.7 Lion

By Chris | Published: July 20, 2011

Lion was released through the App Store earlier today.

Although MacVector has not gone through a full round of testing, our initial tests on development builds and the released version shows that there are no bugs, or at least no obvious ones!

Here’s the coolest feature of Lion, Mission Control.

Lion

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Updated Restriction Enzyme files

By Chris | Published: July 20, 2011

There are a few updated restriction enzyme files available for download.

This file contains the latest Gateway and TOPO sites, and this file is contains the Common Enzymes file together with the updated sites.

You can read about how to do Gateway cloning with MacVector here.

Incidentally you can select multiple sites for copying by drag-selecting, you just can’t use <SHIFT> – select or <COMMAND> – select in MacVector 12 and earlier. We’ve rewritten the Restriction Editor window for our upcoming MacVector 12.5 release and it now uses a standard OS X Cocoa TableView, so you get all the usual selection behaviour you’d expect in a normal list.

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Hiding Tooltips in the Editor.

By Chris | Published: July 11, 2011

A feature new to MacVector 12 is the ability to both annotate and display features directly in the Editor, without having to open a separate Map view window.

There are also tooltips that show the feature on the sequence directly under the mouse cursor. For example in the following screenshot you see the ID of a CDS feature annotated on the sequence.

MV12 EditorPopup

Sometimes this can obscure the sequence underneath, so press the “Escape” key to hide the popup.

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MacVector 12: Drag and Drop annotation of your sequences

By Chris | Published: July 6, 2011

This is in a series of blog posts on interesting highlights of new features added to MacVector 12

If you click and drag a result from a results map to a sequence window it will be annotated as a feature. For example dragging a primer from a primer results map will annotate that primer as a MISC_BINDING feature in the sequence (see the screenshot where the PCR product has been annotated).

Once a result has been annotated it will be hidden from the results window to avoid adding it in duplicate.

Incidentally as well as dragging and dropping results, there’s many other places where drag and drop has been added to MacVector over the past few releases.

Oh and do remember that ALL annotation created from within MacVector is fully compliant with the Genbank Feature table specification.

MV12 DragDrop

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Changes to isoelectric point calculation in MacVector

By Chris | Published: June 27, 2011

We have a policy of constant improvement in all areas of MacVector, even with algorithms and analyses that have been the same for many years. Recently we changed the way that the isoelectric point of a protein was calculated. The previous version of the algorithm was accurate for short proteins, however for longer amino acid sequences the values were not as accurate as they should have been. There were three problems that caused this discrepancy:

(a) using some out of date values for pI,

The pI values for each residue were not as accurate as they should have been. The upper set is the old values, the lower set are the new ones. Additionally we also did not calculate for Cys;


Asp   Glu    Tyr     Lys    Arg    His   Cys   NH3  COOH
3.86, 4.25, 10.10,   9.80, 12.48, 6.00, n/a,  8.00, 3.00

Asp   Glu    Tyr     Lys    Arg    His   Cys   NH3  COOH
3.90, 4.07, 10.46, 10.54, 12.48, 6.04, 8.18, 8.20, 3.65

Incidentally the latest values are actually taken from the Wikipedia page. Many different sources were reviewed, however, we discovered a fair amount of discrepancies between many sources. Wikipedia seemed to have the most common values so these values were used. The algorithm itself is unchanged and should give the same results as the Expasy server in theory, as both use the same approach. However, in real usage there are slight differences.

(b) using inaccurate values for each amino acid’s molecular weight (only going out to 1 decimal place rather than 4 or 5)

Here’s the raw data for molecular weight; With the old values in column one and the new values in column two. The values are taken from www.webqc.org/aminoacids.php

0.0,

0.0,

A

71.07

71.07822

C

103.13

103.14372

D

115.08

115.08792

E

129.11

129.11462

F

147.17

147.17472

G

57.05

57.05162

H

137.14

137.13992

I

113.15

113.15832

K

128.13,

128.17292

L

113.15

113.15832

M

131.19

131.19712

N

114.10

114.10312

P

97.11

97.11572

Q

128.13

128.12982

R

156.18

156.18642

S

87.07

87.07772

T

101.10

101.10442

V

99.13

99.13162

W

186.22

186.21092

Y

163.17

163.17412

B

114.59

114.10312,

Z

128.62

128.62222

X

110.00

118.836325

0.0

0.0

The old and new values are pretty close, however, the small errors build up over a couple of thousand residues.

(c) The third issue was that it used 32 bit “short float” variables which again lost accuracy with larger proteins.

The calculations now use 64 bit floating points variables.

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Roaming Network Licenses

By Chris | Published: June 20, 2011

We’ve recently introduced a new feature to make using a network license much more flexible. Network licenses are great for sharing licenses amongst a large number of users. However, if you are not physically located in the same building (i.e. connected to the LAN) then it’s not straightforward. For example if you want peace and quiet to write that paper at home or you are at a conference. We aim to make life as easy for the user as possible and so we’ve just introduced a new option for such users.

Our new “roaming network license” works exactly the same as a network license until the user’s Mac can no longer connect to the License Server. Then it will switch to being a standard license for 21 days or until the user reconnects to the network. That means the user can work offsite with MacVector. The user must reconnect to the License Server before those 21 days have elapsed.

The advantages are:

- Any user can use the license for up to 21 days outside of the institute.

- the total number of users inside the institute remains the same regardless of how many users are “roaming” outside the institute.

- The process is transparent to the user and requires no configuration beyond the initial setup.

- To switch to the roaming license the user needs to simply restart MacVector when they are away from the network.

- There is no system reconfiguration needed other than activating the client with a new license code. The same as you do every year when renewing maintenance. Plus this can be pushed out to each Mac transparently to the user.

If you have an active 15 user network license, then contact us to exchange this for free. We will ask you if you want to do this when you next renew. If you have less users then for five users or more we will give you this for the price of a single extra seat. For example a ten user roaming license would be the same price as a 11 user non-roaming network license.

Contact support@macvector.com if you want to activate this for your license.

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