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: sequencing

Generating a primer report to send to your Oligo Synthesis service

QuickTest Primer is a great tool for primer design. Paired with Primer Design/Test (Pairs) it gives you great control and flexibility for designing primers with tails, mismatches, silent mutations, one out sites and more. Once you’ve designed your primer the next step is to get it synthesized. QuickTest Primer will produce a PDF report of […]

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Confirming a small sequencing project against a reference sequence

Align to reference is a perfect tool for mapping small sequencing projects against a reference sequence. It’s perfect for accurately and quickly: – Confirming the sequence of a cloned fragment – Sequencing across the ends of a cloned fragment to confirm the junction sequence – Screening clones from a site-specific mutagenesis experiment to identify successful […]

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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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Save trace files as images

You can open ABI chromatogram (“Trace”) files directly in MacVector and analyze them like any other sequence. You can also use them in the Align To Reference and Assembler interfaces, where the actual trace data will be displayed, or in any other function that accepts external sequence files. Sometimes you just want to print out, […]

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Quickly checking a small sequencing project

For analyzing large sequencing datasets you need Assembler. However, many times you do not need a powerful tool but just a quick way to check some sequencing data. For example for checking small sequencing projects, such as a site directed mutagenesis, looking for SNPs in a PCR product, cloning a gene or checking your latest […]

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Viewing raw chromatogram data from .ab1 files

If you are interested in looking for or evaluating mixtures of residues in .ab1 or .scf chromatogram files, it is important to be able to extract the raw data from the four traces. You can open .ab1 and .scf files directly in MacVector by using the File | Open menu item or by dragging files […]

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How to remove gaps from a sequence

There are often times when you end up with a sequence containing gaps, especially if you make extensive use of the Align To Reference, Contig Assembly or Multiple Sequence Alignment interfaces to generate consensus sequences. You can select and copy the consensus sequence, or even individual aligned reads, from the Align To Reference and Contig […]

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Use Analyze -> Align To Reference to align ABI trace files

One of the most common tasks in any molecular biology lab is the need to re-sequence a piece of DNA. Perhaps it is a cloned PCR fragment where you want to confirm the sequence, perhaps you are sequencing across a cloning junction, or maybe screening clones for a successful mutagenesis experiment. Many users immediately think […]

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101 things you (maybe) didn’t know about MacVector: #18 – Aligning Chromatogram (ABI) Sequences

I blogged about this a few years ago, but its something that still comes up on a regular basis. The blog link discusses the 6 main alignment algorithms in MacVector and how to decide which is the most appropriate for accomplishing different tasks. One common request we get is “I want to see my chromatograms/traces […]

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