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Category: Tips

  • Screening for CRISPR Indels using Align To Reference

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    Chris
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    MacVector’s Analyze | Align To Reference… tool is ideal for screening reads for the short insertions, deletions or substitutions resulting from CRISPR experiments. Simply open your reference sequence, choose Analyze | Align To Reference…, click on the Add Seqs toolbar button to add reads from different clones/experiments, then click on Align to align the reads…

  • How to align DNA sequences based on their amino acid translations

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    Chris
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    A new tool in MacVector 15 allows you to align DNA sequences based on their amino acid translated sequence. For most alignments in MacVector you will use the Multiple Sequence Alignment tool. This allows you to align DNA or protein sequences using either Muscle, Clustalw or T-Coffee. MacVector 15 now allows you to align DNA…

  • Functional domain analysis of protein sequences using InterProScan

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    Chris
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    There’s a new tool in MacVector 15 that allows you to do functional domain analysis on your protein sequence using the InterProScan service. InterPro contains multiple databases of protein families, domains and motifs and InterProScan will submit a protein sequence to a search of these databases. It will also do extra analysis such as transmembrane…

  • Create your own Primer Database.nsub from an Excel spreadsheet

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    Chris
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    EDIT: MacVector 18.6 onwards will natively import primers in spreadsheets. Wouldn’t it be great if there was an easy way of converting that huge primer collection you have into a format that MacVector can use? Well, luckily there is! There is a utility called “Primer Converter” that you can download from our website. To use…

  • Use Analyze->Primer Database Search to scan sequences for primer binding sites

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    Chris
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    It’s easy to keep track of all your primers using a MacVector subsequence (.nsub) file. We even ship MacVector with a starter file called “Primer Database.nsub” that you can find in the /Applications/MacVector/Subsequences/ folder. If you choose Analyze | Primer Database Search… and use this default file to search pUC19, you’ll find many of the…

  • Viewing external database entries for features in a sequence.

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    Chris
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    Sequences, or regions of sequences, can be linked to external databases. For example an entire sequence entry or for when annotation tools are used to annotate proteins with domain or motif information (e.g. InterProScan available in MacVector 15). Very useful for when you want to view more detailed or updated information. Within the Genbank specification,…

  • Optimizing the Reverse Translation function

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    Chris
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    The Analyze | Reverse Translation menu option lets you create a DNA sequence from a Protein sequence, reverse translated using a specific Genetic Code (by default, the Universal Genetic Code). The default option creates a DNA sequence with N’s and other ambiguities reflecting the degeneracy of the genetic code. This is great if you want…

  • Tear-off Result Window Tabs: make viewing results easier.

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    Chris
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    All analysis results for an individual sequence are collected into a single tabbed result window to reduce window clutter. However, there are times when it is very convenient to have results displayed in side-by-side windows. For example, if you run a dot plot you can zoom in to view sections of the comparison by drag-selecting…

  • Highlighting sequence using color and lower case in the Editor tab

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    Chris
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    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. To color a region. To change the case of a region.

  • Estimating insert length quickly for a read pair

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    Chris
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    [Edit December 20, 2017 – As of MacVector 15.5 you can simply right click a READ and select “SEE MATCHING READS” to view the pair of reads. The total sequence length is selected. ] Insert length is the length of the sequence in between a pair of reads. Sequencers are supplied DNA samples in fragments of…