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: sequence editor

Use File->Export in the Contig Editor to save selected reads

Last week we covered the fact that you can use File->Export to save sequences or alignments in different formats. Delving down deeper into this, some of the views will save different types of data based on what you select in the format menu. The best example of this is the Contig Editor. If you choose […]

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Highlighting sequence using color and lower case in the Editor tab

You can very quickly annotate a region of interest in your sequence in the Editor tab. For example, showing introns in lower case or highlighting CDS features with a colored background. Using the TRANSFORMATIONS menu To enter sequences as mixed case. Enable Edit | Transformations | Enable Mixed Case Entry Type your sequence using SHIFT […]

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How to reset the sequence numbering when working with a subsection from a larger sequence

When you copy a section from a long sequence and paste it into a new MacVector window, the original numbering from the original sequence is retained. This is very useful if you want to work on a shorter segment of a genome without losing the original numbering. However, sometimes it is preferable to have the […]

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Quick shortcuts to zoom in and out in the Single Sequence Map tab

One very useful feature of the single sequence Map tab is that you can use the mouse to “drag-select” and zoom in to view a smaller section of a large sequence. Apart from the utility of using this to “drill down” to view individual genes, or even residues, in a large sequence, if you do […]

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Opening matching sequences from an Align To Folder search

You can use the Database->Align To Folder menu function in MacVector to quickly search any set of folders on your hard drive for matching sequences. Its like having your own personal BLAST search that just scans files of interest to you. The great thing is, when you find matching sequences, you can easily open them […]

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How to reset the numbering after pasting a DNA fragment

When you copy a section from a long sequence and paste it into a new MacVector window, the original numbering from the original sequence is retained. This is very useful if you want to work on a shorter segment of a genome without losing the original numbering. However, sometimes it is preferable to have the […]

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How to display translations in the sequence editor

For those of you who like to type in DNA sequences, or do manual editing to the sequences, it’s really useful to be able to see the translations above or below the sequence residues in the Editor tab of the single sequence window. If you are a long term user, you’ll be familiar with the […]

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101 things you (maybe) didn’t know about MacVector: #13 – Lower Case Sequences

By default, MacVector uses upper case letters for sequence residues. However, you can also use lower case characters if you wish. Changing the case of residues does not affect the MacVector analysis algorithms – GAATTC, gaattc and gAAttC are all considered valid EcoRI sites for example. If you want to set a short region of […]

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101 things you (maybe) didn’t know about MacVector: #10 – Displaying Amino Acids As Triple Letter Codes In Translations

Following on from my last post about turning on translations in the sequence Editor, I thought I should point out how to display amino acid translations using the 3-letter code rather than the default single-letter code. I don’t know about you, but I have a hard time remembering that “W” is the single-letter IUPAC code […]

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101 things you (maybe) didn’t know about MacVector: #3 – The Importance of Topology

MacVector understands the difference between circular DNA molecules and linear DNA molecules. Not just from the standpoint of how the molecule is displayed on the screen, but also in regard to how the analysis algorithms handle the junction at the ends of the circle. The Topology button controls the underlying linear versus circular state of […]

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