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!

Author Archives: Chris

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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Use File->Export to save sequences in a different file format

Over the years, Apple have changed the recommended layout and functionality of the File menu. At MacVector, we always try to follow Apple’s guidelines wherever possible so that new users will feel comfortable with familiar menus. However, long-term users may experience some confusion, particularly if you want to save sequences in a different format. Here […]

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How to reset the graphics palette if it disappears

The floating graphics palette is extremely useful for helping to configure the display of the Map tab. You can easily toggle the visibility of any individual or group of features and adjust many aspects of the display. MacVector does try to remember the last position you moved this to so its there ready for you […]

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Tips for finding ORFs in your sequence

We’ve talked in previous tips about annotating open reading frames as CDS features. However, what if your sequence has no annotated ORF? MacVector’s ANALYZE | OPEN READING FRAMES… tool will help you find any quickly. However, if you are new to this tool there are a few options that may prove initially confusing. These options […]

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Using QuickTest Primer to check for hairpins in sequences, and not just primers.

Although QuickTest Primer is intended for designing primers, the interface is very flexible. If your sequence is not too long, you can use the Quickest Primer interface to scroll through a sequence and visually look for hairpins appearing in the hairpin pane. The easiest way to do this is to select the first ~100 nt […]

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Download the latest published version of your favorite sequence with its accession number

It’s very quick to download the latest version of a sequence if you know its accession number. When you start working with a new sequence, it’s the best place to start. Go to DATABASE > ENTREZ Enter the accession number of your favorite sequence Click SEARCH Double click on the result to open up your […]

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Customizing BLAST alignment results to make mismatches more noticeable

When you run a Blast search, as well as a list of hits, you will get a list of alignments between your query sequence and each hit. As with most other text alignments in MacVector, identical matches are by default represented by a vertical line (a score greater than 1) and mismatches (whether similar or […]

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How to save contig consensus sequences from assembly projects

The MacVector Assembler module lets you create projects, populate them with Sanger Sequencing or NGS data files (or any sequences in a format that MacVector can read) and then assemble them using the popular phrap and/or Velvet assemblers. Typically, the result will be a collection of contigs that you might want to use in additional […]

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Search fastq files and retrieve matching reads into paired fastq files

The Database | Align To Folder… function is essentially your own personal BLAST search of sequences on your computer, but with the advantage that you can scan fasta/fastq containing millions of entries and retrieve matching Reads into a new file. MacVector 14.5 added an enhancement where you can search paired-end read files and retrieve both […]

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How to retrieve BLAST hits from the Aligned Sequences result tab

After a BLAST search, you can retrieve matching sequences from the Description List results tab. What you may not know is that you can do a similar thing from the Aligned Sequences result tab. One advantage of this approach is that (as in the example above) sometimes there are multiple accession numbers for a hit. […]

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