Category: 101 Tips
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101 things you (maybe) didn’t know about MacVector: #52 – Data mining to identify and analyze pangolin CoV-2 analogs to the human COVID-19 virus
One of the most underrated features in MacVector is the Database | Align to Folder function. You can use this as a more sensitive version of a local BLAST search to find sequences in a “database” that match a query sequence. But in this case the “database” is simply a collection of your own sequences,…
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101 things you (maybe) didn’t know about MacVector: #51 – Rapid assembly of genomes with Velvet and SPAdes
Not so long ago, to assemble even a small genome with Next Generation Sequencing data required an array of clustered computers and a lot of patience. But improvements in algorithms and hardware mean that it is now realistic to assemble bacterial genomes, or even smaller eukaryotic genomes using MacVector on a modest laptop machine. MacVector…
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101 things you (maybe) didn’t know about MacVector: #50 – Using Align To Folder to “clone” genes from NGS data
The Database | Align To Folder… function in MacVector is remarkably powerful. Its like having your own personal BLAST search except that it can also scan through millions of Reads in fasta or fastq formatted files to identify those matching an input sequence, which can be DNA OR protein. In addition, it understands about paired-end…
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101 things you (maybe) didn’t know about MacVector: #49 – Identifying CRISPR Indels
If you are screening a set of clones for the presence of changes after a CRISPR experiment, then the MacVector Analyze | Align To Reference functionality is the approach to use. However, you may find that the default parameters are not ideal for this type of analysis – they are tuned for simple sequence confirmation…
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MacVector is designed to be easy to use. Nonetheless there’s a lot of tools and it’s a flaw in most of us that we only stick to doing, what we already how to do. In our busy lives finding time for learning how to do something more efficiently never climbs that growing todo list too…
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101 things you (maybe) didn’t know about MacVector: #48 – Setting the Alignment match/mismatch characters
There are many output windows throughout MacVector that display aligned sequences. If you run an Align To Folder, Create Dotplot or Internet Blast Search, one or more of the output windows will show alignments in a plain text format with some sort of character indicating matching residues. The default is to use the vertical |…
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101 things you (maybe) didn’t know about MacVector: #47 – Optimal PCR Annealing Temperature
I wrote about how MacVector calculates the melting temperature of a primer in an earlier blog post. One other common question we get is, “once I have designed a pair of primers, what is the optimum annealing temperature to use in the PCR?” MacVector calculates this and displays the results in the Analyze | Primer…
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101 things you (maybe) didn’t know about MacVector: #46 – How to increase the number of graphics layers in the Map tab
The graphical maps of heavily annotated sequences can get busy in a hurry. You may end up with so many features overlapping a specific location on a sequence that the graphical images for those features “pile up” on top of one another at the top or bottom of the display. While this can happen with…
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101 things you (maybe) didn’t know about MacVector: #45 – Automatically annotating sequences using BLAST
The Database | Auto-annotate Sequence… tool is a great way to automatically annotate a bare DNA sequence. If you are unfamiliar with this, check out this previous tip. Auto-annotate is an incredibly simple (and fast!) way to annotate a bare sequence, but it does rely on you having a folder full of sequences containing all…
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101 things you (maybe) didn’t know about MacVector: #44 – Opening matching sequences from an Align To Folder search
The Database | Align To Folder function is an extremely useful tool to help you find matching sequences on your own local file system. It is essentially a BLAST search of your own private sequence collection – a little slower, but more sensitive. You can use it to easily open all of the sequences you…