101 things you (maybe) didn’t know about MacVector: #15 – Getting GenBank/Entrez Sequences Into MacVector

MacVector does have a built-in Entrez browser that lets you search the online Entrez GenBank database using keywords and retrieve matching sequences either To Disk or as sequence windows (To Desktop) without needing to leave MacVector. You can access this via the Database | Internet Entrez Search… menu item. I’m not going to discuss how to use that browser in this posting. However, there are times when you may be using a web browser to access the Entrez database, or perhaps a colleague has sent you a file in GenBank format. MacVector supports GenBank formatted files seamlessly – you can simply choose File | Open, navigate to the location of the file, select it and click OK. MacVector will automatically recognize the GenBank format. You don’t have to worry about the file extension – it can be .txt, .gb, .gbk, something completely different (.myseq, .idontknow) or even non-existent. The only important setting is that in the File | Open dialog, you may need to enable All Documents to be able to select files with non-standard extensions;


If you are browsing the Entrez website, it is not actually necessary to specifically download the sequences you are interested in and save them as files on your hard drive. You can actually accomplish this by a simple copy and paste. Lets look at an example;


In this example we have found an interesting sequence (well, interesting to me!) and have it displayed in GenBank format. Note that we have the Show Sequence checkbox selected to make sure we have the sequence displayed in the report in addition to the features. This is often turned off by default for large sequences, so be sure to check. Then we start a text selection by clicking just to the left of the LOCUS text and drag-selecting a few lines. The next step is to hold down the SHIFT key and use the mouse to scroll to the bottom of the window;

Entrez Bottom.png

Still holding down the SHIFT key, click just to the right of the “//” characters indicating the end of the entry. That will select the entire sequence from “LOCUS” to “//”. Then select the Edit | Copy item from the browser menu and switch to MacVector. In MacVector, choose the File | New From Clipboard menu item;


A new sequence window appears, containing not just the DNA sequence, but also all of the features associated with the sequence that were included in the GenBank report. This procedure is effectively the same as saving the GenBank formatted sequence to a file and then opening that file as described above.

SCU03771 ― Map.png

This same approach works for any text-based file sequence format – FastA, EMBL, GCG – that MacVector knows how to read. Simply copy the appropriate text, then choose File | New From Clipboard.

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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