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!

Tag Archives: genbank

Use File -> New From Clipboard to create new sequence documents

Whenever you have information copied to the clipboard, you can choose File | New From Clipboard and MacVector will interpret any data on the clipboard and create a new document of the appropriate type. While this is most commonly used for DNA and Protein sequence documents, this also works for multiple sequence alignments and data […]

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How to import annotated GenBank sequences via copy and paste

While MacVector does have a built-in Entrez browser (Database > Internet Entrez Search) you can easily import GenBank formatted text into MacVector via a simple copy and paste approach. Many sequence-oriented web sites have the option of viewing sequences in GenBank format. This format always starts with the text LOCUS and finishes with two forward […]

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Using Applescript to batch convert files.

Up until MacVector 13 Applescript support was fairly limited. However, with this release we’ve started to expand it. The first enhancement has been to improve the export of files. Now you can export files to any supported format. Over the next few releases this support will be further expanded to include some analysis tools. If […]

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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 […]

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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 […]

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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 […]

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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 […]

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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 […]

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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 […]

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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 […]

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