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!

101 things you (maybe) didn’t know about MacVector: #24 – Creating Features

This is a tip primarily aimed at new users of MacVector, but may be of interest to anyone who wants better understand the way MacVector handles features. MacVector can create wonderfully detailed graphical maps of a sequence, showing all the points of interest, restriction sites, open reading frames etc. However, each item to be displayed (with the exception of automatically generated restriction enzyme sites) must be annotated on the sequence as a feature. If you open any of the MacVector DNA sample files (e.g. pBR322 in the /Sample Files/ folder) you can see a list of all of the features in the Features tab.

pBR322 ― Features.png

MacVector considers any annotation that has a start and/or a stop location on the sequence to be a “Feature”. Other annotations that do not have start and stop locations (e.g. keywords, authors and publications) are displayed in the Annotations tab.

There are a number of ways to create a new feature in MacVector – the simplest is to click on the Create button on the toolbar;

FeatureCreateButton.png

This opens the main Feature Editor;

FeatureEditorEmpty.png

Initially, the start and stop locations are undefined, so you need to click on the plus button to open the Location Editor;

Location Editor.png

Type in the start and stop locations, then click OK. Back in the Feature Editor, choose a suitable Feature Keyword from the drop down menu. The list that appears is always the latest GenBank approved list of keywords. If you are annotating a protein coding sequence, be sure to use the CDS keyword. If you can’t find a suitable keyword in the list, then use one of the misc_XXX features.

There are two options for adding comments to a feature. The preferred approach to be fully GenBank compliant) is to use the Qualifiers tab and click on the plus button to add a new qualifier;

FeatureEditorQualifiers.png

This opens the Qualifier Editor that lets you select and valid qualifier for the type of Feature you are creating.

Qualifier Editor.png

You can add as many qualifiers as you like – the tet CDS in pBR322 has seven different qualifiers representing different information regarding the coding region.

Alternatively, you can enter Free Form text for the feature description;

FeatureEditorFreeForm.png

In this case, the comments actually get assigned to a generic “/note=” qualifier. When you finally click OK, a new feature of that type is created and appears in the Features table and also in the graphical Map tab.

A far more convenient way to create a feature with a specified start and end point is to start with a selection in the Editor or Map tabs. If you then choose the Create button, the Feature Editor will be pre-loaded with the selection, saving the step of opening the Location Editor;

pBR322EditorWithSelection.png
FeatureEditorPreSelection.png

MacVector always remembers the last Feature Keyword you used, again saving time if you are creating a lot of new similar features.

In the next post, I’ll discuss some of the shortcuts in MacVector for quickly creating features from the results of various analysis functions.

This is an article in a long running series of tips to help you get the most out of MacVector. If you want to get notified every time a new tip gets published, follow us @MacVector on twitter (or check the feed for the hashtag #101MacVectorTips) or like us on Facebook.

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