Importing sequences from ENSEMBL

There’s a few different ways to import annotation from the ENSEMBL database browser, as well as other databases. Using Genbank The easiest way to export from ENSEMBL and keep all annotation is to use the Genbank format. The default format will be FASTA which has no annotation. With Genbank all the annotation is stored in […]

Posted in Tips, Tutorials | Also tagged | Comments closed

The oldest entries in Genbank? Some fun for Labor day.

Inspired by some tweets from @ewanbirney, because I’m waiting for lunch and because it’s Labor Day I used the Entrez tool to find the oldest entries (using the publication date field) in Genbank. For proteins there’s a single hit in 1979 For NA there’s 12 hits from 1982: Nothing useful here and it’s probably not […]

Posted in Uncategorized | Also tagged | Comments closed

101 things you (maybe) didn’t know about MacVector: #30 – Submitting Sequences To GenBank using Sequin

Note: while preparing this blog post we discovered a bug in MacVector 12.7.4 that prevents submission using the exact steps shown here. Be sure you are using MacVector 12.7.5 or later which has the bug fixed. If you are using an earlier version, send an e-mail to support@macvector.com and we’ll send you the details of […]

Posted in 101 Tips | Also tagged | Comments closed

101 things you (maybe) didn’t know about MacVector: #25 – Creating Features from Analysis Results

In my last post I described how you can quickly create and annotate features onto a DNA sequence, although the post was primarily aimed at users who are new to MacVector. In this post I’ll take a look at how you can quickly and easily annotate a DNA sequence with features based on the results […]

Posted in 101 Tips | Also tagged , | Comments closed

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 […]

Posted in 101 Tips | Also tagged | Comments closed

101 things you (maybe) didn’t know about MacVector: #23 – Viewing Publications

If you ever download sequences from Entrez, or open a GenBank formatted sequence file, you will often see PUBMED entries in the Annotations tab with blue colored numeric IDs; The blue color indicates that this is a link that you can use to retrieve an abstract of the publications. If you double-click on the PUBMED […]

Posted in 101 Tips | Tagged | Comments closed

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 […]

Posted in 101 Tips | Also tagged | Comments closed

101 things you (maybe) didn’t know about MacVector: #12 – Displaying Segmented Features

While most features you might encounter in DNA files have a simple start and stop location on the sequence, some features are segmented. For example, the coding sequence of a protein encoding reading frame containing introns is represented by a segmented CDS feature on the genomic DNA. MacVector has always understood that the individual segments […]

Posted in 101 Tips | Also tagged , , | Comments closed

MacVector 12: Drag and Drop annotation of your sequences

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 […]

Posted in Releases, Tips | Also tagged | Comments closed

MacVector 12: Annotating the sequence in the Editor View.

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 […]

Posted in Releases, Tips | Also tagged , , | Comments closed