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.
Sometimes this can obscure the sequence underneath, so press the “Escape” key to hide the popup.
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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.
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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(a) using some out of date values for pI,
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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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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The ASM2011 was a great show. We had a busy booth with some old friends and some new faces. We learnt more about what users need and some of that feedback has already gone into our next release, MacVector 12.5, that will be out towards the end of the Summer. We had fun outside the hall as well. New Orleans is a great city with friendly people, although I never could understand why those guys on the moonwalk knew where I got my shoes.
As with the past few years many people were asking whether we run on Windows (we will soon) and can we deal with the gazillion reads of their favourite organism’s genome that they’ve just been given and do not know what to do with (also coming soon). We’ll be adding reference assembly to Assembler 12.5 that will be great for these bacterial genomes.
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It looks like the flood waters will not be a problem for this year’s American Society of Microbiologists 2011 conference In New Orleans. So we’re brushing up our Yat and looking forward to some creole and cajun cooking. If you are also in New Orleans, please do come by and visit us on Booth #1128. We’ll be demoing the latest version of MacVector, as well as looking to chat with users. Come pick up one of our ever popular mousepads too! Not just a conference freebie, but actually useful by the lab computer.
The conference Twitter hashtag is #asm2011 and if we get a few quiet minutes we’ll try putting updates, perhaps even photos, out there. You can follow us for updates and news on MacVector.
Here’s our booth from Philadelphia 20009
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We would like to announce a new license type that is now available – a personal license. This license is perfect for the user who only needs MacVector on one computer. It is perpetual (lifetime), will be node-locked to run only on one machine, and is less than half the cost of a standard license. To refresh your memory, standard licenses with the same serial number can be installed on as many machines as you need, but if the machines are on a local network, they will only run one at a time. In the future, if you wish to be able to use the license on more than one machine, you can upgrade it to a standard license. You may also purchase more than one personal licenses, if you want each computer to have it’s own copy of MacVector. If you would like more details, please contact your regional account manager or email sales@macvector.com.
MacVector has always given the user great control in being able to customise the map’s appearance. By default the label will show the full text description of a feature and all its qualifiers (see the first metatag in the list below). However, the label can contain whatever text you want it to display. Obviously you do not want to waste lots of time changing multiple labels and so MacVector has metatags to define the information that is placed inside the Label. For example using the code below will show the name and location of a feature. Incidentally this is the default label for restriction enzyme sites as shown in the screenshot below. Note that unique restriction enzyme sites (shown in red) only have the <Description><Start> metatags.
<Description> (<Start>) <Index>/<Count>
The full list of metatags is:
<Description> or <Desc> the text of the description associated with a feature replaces this tag. In the case of a Restriction Enzyme, this is the name of the Enzyme.<Start> displays the start location of the feature (for an RE that is the cut site).<Stop> displays the stop location of the feature (for an RE that is the cut site and is identical to <Start>).<Size> displays the size of a feature.<Length> (functionally equivalent with the above metatag).<Type> – substitutes the type of feature e.g. “CDS”, or “mRNA” or “source”.The following metatag applies only to feature graphic types and is disabled for others:
<Segment> shows the position of this feature in multi-segmented features.The following three metatags apply only to restriction enzyme cut sites and are disabled for other features:
<Total> shows the count of this particular feature type.<Count> shows the count of this particular feature type (functionally equivalent with <Total>).<Index> shows the order of an individual feature in the above number.Incidentally the last three metatags do provide very useful information on restriction enzyme cut sites, especially for cloning.
e.g. <Desc> (<Index>/<Total>) would generate labels like “BamHI (1/3)”, which means it’s the first cut site our of a total of three, “BamHI (2/3)” second of three etc.
You can also use metatags to display subsets of information in the feature description using qualifier information. Qualifiers are GenBank tags that supply extra information about a Feature keyword other than the type and location that are already supplied. Some Feature Keywords have mandatory qualifers, whereas some are entirely optional and can have none. For example the Feature Keyword CDS might contain the Gene name (/gene), the translated product (/product), the actual translation (/translation) and perhaps even the protein’s function (/function). As an example of a mandatory qualifier the Source Feature Type must contain the /organism qualifier. You can read the full set of Feature Keywords and Qualifiers on the NCBI’s Feature Table page.
The <Description> metatag displays the entire set of Qualifiers. Using the actual qualifier as a metatag will just use that specfic piece of information instead. For example <gene>(<number>)” will display My Gene (1) if the qualifiers /gene=”My Gene” and /number=”1” are present in the feature description. Using a specific qualifier usually provides a far more succinct label than the full <Description>, particularly for feature-rich sequences imported from GenBank or Entrez. Please note that Qualifier based meta-tags are skipped if the qualifier doesn’t exist in the feature description.
Metatags are case insensitive and if a metatag is not found it will be removed from the label string.
Finally to make all this easier there is a popup menu in the Feature Symbol editor that lets you view all of the available meta-tags and insert them into the label. Click on the small triangle to the left of the label edit box.
We’re all different and one researcher’s preferred way of viewing their sequence may be the opposite of their lab mate’s. With MacVector we try to give you the flexibility of viewing a sequence how you want you view it. With the replica button it’s easy to show multiple views of the same sequence. With a couple of clicks you can view your sequence map AND your sequence at the same time. If you want to that is!
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This is in a series of blog posts on interesting highlights of new features added to MacVector 12
In the last survey a popular request was to be able to change the case, alter the colour, or otherwise being able to annotate sequence directly in the Editor view. You’ve been able to use the Map view to represent features at a sequence level for many versions now. However, we do try to give the user the flexibility to display and work with their sequences the way they want so we’ve added the ability to easily annotate the sequence in the Editor view.
Now the Transformations menu allows you to modify the appearance of the sequence directly in the Editor view. You have control over the case of the sequence in the editor and you can also colour the background or the characters over a range. Note that when you colour part of the sequence, a new feature is created behind the scenes to store this information. When activated, any feature that is visible in the Map View will also cause that region of the sequence in the Editor View to be coloured by the “Fill” colour assigned to that feature. You can display colours by changing the font colour (as in the screenshot) or change the background instead. You can also disable it completely. A sequence may also be entered in mixed case where the case of the sequence will be preserved and displayed in the editor.
To enable this:
– Open the MacVector | Preferences | Colors pane.
– Switch Sequence Editor to show Color Background or Color Sequence
To enter sequences as mixed case:
– Enable Edit | Transformations | Enable Mixed Case Entry
To disable sequence being entered as mixed case:
– Disable Edit | Transformations | Enable Mixed Case Entry
To color a region:
– Select the region.
– choose Edit | Transformations | Color.
To change the case of a region:
– Select the region you want to change to lower case
– choose Edit | Transformations | Make Lower Case.
If you have not yet done so download your MacVector 12 updater.
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