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101 things you (maybe) didn’t know about MacVector: #49 – Identifying CRISPR Indels
Read more: 101 things you (maybe) didn’t know about MacVector: #49 – Identifying CRISPR IndelsIf 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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How to use Codon Preference plots
Read more: How to use Codon Preference plotsWhen you are looking for open reading frames in newly sequenced regions, it’s not always the longest ORFs that are protein-encoding. Lets look at an example from one of the sequences included with MacVector: /Applications/MacVector/Sample Files/Gal Cosmid.nucl. This is from Streptomyces coelicolor, a filamentous bacteria with a 73% G+C content. The high G+C% means that…
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MacVector 15 is out, with a focus on protein analysis and alignment tools.
Read more: MacVector 15 is out, with a focus on protein analysis and alignment tools.MacVector 15 has many new features including new protein analysis tools for reference alignment of proteins, translated DNA alignments and for functional analysis of protein sequences. InterProScan: Scan proteins for functional domains against a variety of sequence, protein family, domain and motifs databases using the InterProScan service. This performs a search against many different databases…
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Tweak your DNA Matrix for better Align To Folder searches with primers
Read more: Tweak your DNA Matrix for better Align To Folder searches with primersYou can use the Database | Align To Folder function as your own “personal BLAST search”, comparing a sequence to all of the sequences in a target folder hierarchy. The files in the folder can be in any format MacVector recognizes, including fasta and fastq formatted multiple sequence files. Many users take this approach to…
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How to reset the sequence numbering when working with a subsection from a larger sequence
Read more: How to reset the sequence numbering when working with a subsection from a larger sequenceWhen 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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Organising your sequences using Smart Folders
Read more: Organising your sequences using Smart FoldersOS X’s Finder has many features for quickly finding and working with your files. Spotlight Search is one such tool that most Mac users are familiar with. However, Smart Folders is a tool that is very useful but often overlooked. Smart Folders allow you to create a dynamic folder whose contents are derived from a…
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How to increase the number of graphics levels to stop features overlapping.
Read more: How to increase the number of graphics levels to stop features overlapping.MacVector tries to optimize the Map graphics layout using a trade-off between performance and minimizing unnecessary white space. Sometimes the default settings we have chosen are not ideal, particularly if you are looking at the Map tab of an Align To Reference window where you have a large number of reads overlapping the same region.…
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Know Your Alignments
Read more: Know Your AlignmentsWe often get asked “how do I do an alignment” using MacVector? Well, the answer to that is always “it depends”, and it depends on what you want to learn about your sequence(s). Here’s a quick summary of the different types of alignments and what you would use them for: Multiple Sequence Alignment (File |…
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Importing sequences/features from websites such as ENSEMBL or UCSC’s Genome Browser
Read more: Importing sequences/features from websites such as ENSEMBL or UCSC’s Genome BrowserMany Genome Browsers/databases allow you to browse and view genomes, or a specific gene/region, with a high degree of detail. For example ENSEMBL and the UCSC Genome Browser. However, many times you want to work with that data on your own Mac. As usual the easiest way to exchange sequence data is using the Genbank…
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How to reset the zoom level when you Drag Zoom into your sequence.
Read more: How to reset the zoom level when you Drag Zoom into your sequence.Being able to Drag Zoom makes it easy to view a specific region of your sequence in greater detail. To Drag Zoom, just hold down the mouse button and drag the cursor along your sequence. The Map view will redraw to show the selected area in greater detail. Once you are zoomed in you have…
