Opening multiple sequences as alignments or individual sequences

By Chris | Published: April 10, 2018

Many sequence formats contain multiple concatenated sequence entries. For example FASTA and Genbank are two formats capable of storing multiple individual sequences.

By default MacVector will treat such sequences as alignments and open them in the Multiple Sequence Alignment editor. Most users who want to open such a file do want to see an alignment. Additionally if the default behaviour was to open as individual sequences, then accidentally clicking on a large alignment would result in many hundreds of individual sequence windows opening up on your desktop (do remember that holding down the OPTION key and clicking on the close button will close all open sequences).

If you need to open such a sequence file as individual sequences, then there’s a simple option that you need to check in the FILE | OPEN dialog. This behaviour has not changed for quite some time. However, back in MacVector 13 the appearance of the dialog changed, due to a change in Apple’s current guidelines on file dialogs. Whereas the older dialog had an obvious way to see this dropdown menu, now all you see is a small OPTIONS button in the bottom left hand corner.

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To open multiple sequence files as individual files you need to check an option in the FILE | OPEN dialog.

  • Click FILE | OPEN
  • In the dialog click OPTIONS (bottom left corner)
  • Change OPEN MULTIPLE SEQUENCE FILE AS from AUTO to SINGLE SEQUENCES
  • Click OPEN
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    Restoring file associations when MacVector no longer opens your sequences

    By Chris | Published: April 5, 2018

    Macs are pretty good at choosing the right application to open a document. For example when you double click on a .nucl document then it will open in MacVector. However, sometimes this file association breaks. Applications should coexist peacefully on a Mac, but sometimes a misbehaving app will corrupt these file associations and you will find that your sequence displays a generic document icon (or what’s worse a different application!). When you double click on the icon, it will no longer open in your favourite DNA sequence analysis tool!

    Luckily this is easily fixable:

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    1. Select a .nucl file in the Finder
    2. Choose File | Get Info (or use command-I).
    3. In the “Open with” section, click on the popup menu and select MacVector
    4. Then click on the Change All… button to apply the change to all files.
    5. Repeat for all file types used by MacVector that are not opening correctly (e.g. .prot, .msan, .msap, .axml)
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    What can MacVector do for me?

    By Chris | Published: April 5, 2018

    Here’s what MacVector can do for your lab.

    Comparing sequences

    Whatever type of alignment your sequence needs, there’s a tool in MacVector.

    Cloning

    CRISPR Indel Analysis: Identify insertions and deletions following CRISPR editing of a target.

    Sequence assembly of NGS data against a reference genome or compare your sequencing against your new construct.

    Translated Multiple Sequence Alignments: Align DNA sequences based on their translations.

    Align proteins against a reference great for comparing known proteins against an unknown one.

    Auto Annotation of common plasmid features to blank sequences.

    InterProScan: Scan proteins for functional domains against many databases.

    Cloning

    MacVector

    Design Cloning workflows

    As simple as dragging a fragment to a cloning vector.

    Flexible Cloning Subclone with restriction enzymes, Gibson cloning, Gateway and more.

    Cloning history Every step is documented.

    Agarose Gel to run out digested sequences. Easily identify site(s) to differentiate successful clones.

    Primer Design

    Design primers with ease.

    QuickTest Primer changes primer design. Hairpin? Nudge your primer until it goes.

    Add tails to your primers with silent restriction sites/mismatches and view reading frame changes.

    Quickly design pairs of primers click a region to get the best primer pairs to amplify it.

    Primer Database store your primers and scans sequences for potential binding sites.

    MacVector

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    Searching and downloading sequences from Entrez

    By Chris | Published: January 26, 2018

    MacVector has integrated connectivity to the NCBI BLAST and Entrez databases. You can directly search Entrez for DNA or Protein sequences based on features, authors, keywords etc and directly download them into MacVector, complete with all features and annotations.

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    Eastern Great Lakes workshop tour in February

    By Chris | Published: January 25, 2018

    The MacVector team will be touring the Eastern Great Lakes for a series of workshops in February.

    We will be running workshops in Rochester NY, Buffalo NY, Ypsilanti MI, Cleveland OH, Wooster OH, Columbus OH and Cincinnati OH.

    Monday, Feb. 5th

  • 10:00 – 12:00 University of Rochester, Rochester, NY
  • 2:00 – 4:00 University at Buffalo, Buffalo, NY

    • Tuesday, Feb 6th

  • 10:00 – 12:00 Wayne State University in Detroit, MI
  • 2:30 – 4:30 Eastern Michigan University, Ypsilanti, MI

    • Wednesday, Feb 7th

  • 10:00 – 12:00 Cleveland Clinic Foundation, Cleveland, OH
  • 2:00 – 4:00 College of Wooster, Wooster, OH

    • Thurs. Feb. 8th

  • Nationwide Children’s Hospital in Columbus, OH.

    • Friday, Feb 9th

  • 11:00 – 1:00 Cincinnati Children’s Hospital Medical Center, Cincinnati, OH

    • In workshops we try to highlight the new functionality introduced over the last few years to MacVector that even more experienced users may not be familiar with. The format is very informal and participants are encouraged to ask questions and help direct the workshop towards areas of the most interest. We’ve found that every workshop we have run has helped users make the most of MacVector.

    (more details to follow).

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    Using MacVector’s Auto Annotate tool to annotate blank sequences.

    By Chris | Published: January 10, 2018

     

    Have you ever been sent a plain unannotated sequence, or downloaded a sequence from Entrez and been disappointed as it doesn’t have the carefully curated graphical appearance of your favorite genes? Auto annotation solves both of these common problems. The basic idea is that you can scan the sequence against a folder containing a collection of existing annotated sequences and MacVector will find the matching features in the folder and add those to the starting sequence.

    Posted in Tutorials | Tagged , , | Comments closed

    Adding a primer to MacVector’s Primer Database.

    By Chris | Published: January 10, 2018

     

    MacVector’s Primer Database tool makes it easy to store your lab’s regular primers. It allows you to save and retrieve primers from the Primer Database from the Primer3 and Quicktest Primer tools. You can also scan sequences for potential primer binding sites. The Primer Database will also store tails and allow you to specify the maximum mismatches allowed. The tool comes with a starter database of primers, but you can use existing subsequence files or import primers from Excel.

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    RNASeq Expression Analysis with NGS data

    By Chris | Published: December 20, 2017

    If you have the Assembler module, MacVector can align millions of NGS reads from RNASeq experiments against large genomes and generate a coverage table displaying the relative expression levels of every gene in a genome. The key to this functionality is that you must have a reference genome with genes annotated as CDS or gene features – then you can use Bowtie to rapidly assemble reads from fastq files against the genome and generate a report listing the coverage for each feature. The steps to do this are

  • Use File | New | Assembly Project to create a new project.
  • Click on the Add Ref toolbar button to add a suitable annotated reference genome.
  • Click on the Add Reads toolbar item to add your RNASeq reads.
  • Click on the Bowtie toolbar button to assemble the reads against the reference genome.
  • Double-click on the resulting reference contig item and switch to the Coverage tab.

    • You will get a display similar to this.

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    This lists each CDS and gene feature, along with the number of reads that aligned to each feature and the Reads Per Kilobase of transcript per Million mapped reads (RPKM) and Transcripts Per Kilobase Million (TPM) values that can be used to compare expression between genes and runs.

    There is an RNASeq Expression Analysis Tutorial available that describes this functionality in more detail. If you have updated to MacVector 16.0.4 you will find this in the /Applications/MacVector/Documentation/ folder. If you do not have 16.0.4, you can download the tutorial and sample dataset. Although this is a small dataset designed for rapid analysis, you can use this approach to align 50 million+ reads against the entire human transcriptome on a modest (16 GB RAM) MacBook Pro.

    Not sure if you have Assembler? Choose MacVector | About MacVector. If the screen that appears says “MacVector with Assembler, Pro Edition” then you have it. If not, you can sign up for a fully functional 21 day trial version.

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    Annotating primers to your sequence with MacVector

    By Chris | Published: December 8, 2017

    Designing a pair of primers to amplify a single feature is pretty quick with MacVector. Once you have designed a pair of primers with MacVector, you can quickly annotate both the primers and product to your sequence template. The annotation contains a timestamp and the primer’s characteristics. It also contains the full sequence of the primer, which means any custom ends (with mismatches or new restriction sites) are also included.

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    Use a right-click in the Contig Editor tab to see if your contig can be circularized

    By Chris | Published: November 29, 2017

    MacVector 16 incorporates no less than THREE different de novo assemblers, phrap, velvet and SPAdes. While all are great assemblers, with each having their own specific advantages, none of them will generate a circular sequence from input reads. However, MacVector 16 also includes a new feature to help you with this. If you are assembling reads representing plasmid sequences, or if you are closing gaps in a circular genome, you can find out if a contig can be circularized by double-clicking on it in the Assembly Project and then right-clicking* in the Contig Editor to bring up a context-sensitive menu.

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    The algorithm looks for a perfect overlap between the ends of at least 20 bases. If no overlap exists, the menu item is greyed out and reads “Cannot Circularize Consensus“. Otherwise it indicates the length of the overlap. If you select the menu item, a new sequence window opens containing the circularized consensus of the contig, with all gaps removed.

    *To right click with a trackpad hold down [CTRL] and click once or tap with two fingers. MacVector has many “right click” menus with extra functionality.

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