Import Multi-Sequence Genbank Files into an Assembly Project for easy access to Features

There are many genomes in the Genbank database that cannot be downloaded as single annotated sequences. These might be large multi-chromosome eukaryotic genomes, but, increasingly, partially sequenced bacterial chromosomes where the major contigs have been annotated using the NCBI annotation pipeline. Typically, when you encounter these, there are options to download annotated versions of these as multi-sequence Genbank formatted files. MacVector has the option to open any file containing multiple sequences as either a Multiple Sequence Alignment document or as individual Sequence documents. This is not always optimal if you have more than a handful of sequences in the file. However, if you use MacVector with Assembler, you can import these sequences into a project using the Add Ref toolbar button and the individual sequences will not only be displayed in the project window, but, if you double-click on one, the complete annotated sequence will be opened.

Unknown

This is a great way to view and/or sort collections of annotated sequences in Genbank format that cannot be done directly through the Apple Finder. Once opened, you can Export… any sequence in another format if you wish.

Posted in Techniques, Tips | Tagged , , | Comments closed

Opening Genbank or FASTA files with multiple sequences as individual sequences

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, a few versions back the appearance of the dialog changed, due to a change in Apple’s 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.

Unknown

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
  • (Read More…)

    Posted in Tips | Tagged , , | Comments closed

    Optimizing Align To Folder Parameters for use with NGS Data

    You can use the Database | Align To Folder function to scan large fasta or fastq files containing NGS data to find and retrieve just those reads that match a specific target sequence. The search is aware of paired-end reads, so when you retrieve hits, both reads of a pair will be saved into a pair of fasta or fastq files, even if only one of them matched the query sequence. This is a great way of finding sequencing reads to extend any short sequence. For optimum performance, set up the Align To Folder search like this.

    Unknown

    Set the Search Folder to the location of your data and select the Folder contains paired-end reads checkbox if you are working with paired data. For speed, make sure Hash Value is set to the maximum (currently 12) and use a large Scores to Keep value to make sure you can retrieve all the hits. Finally, use the DNA identity with penalties matrix to optimize the search so that only very close matches are reported.

    On a moderate machine (e.g. a three year old 2.7 GHz i7 MacBook Pro), a search of 20 million x 90nt reads with a 500 bp search sequence might take from 45 mins to two hours, depending on the number of hits encountered. To retrieve the hits, select the numbered rows in the Folder Description List results tab and choose the Database | Retrieve to File… menu item. If you used paired-end data, two files will be produced, –1.fastq and –2.fastq, that you can then use as input to Assembler for SPAdes or Velvet assembly, or to Analyze | Align To Reference for more detailed reference alignment analysis.

    Read More…

    Posted in Techniques | Tagged , , | Comments closed

    MacVector and macOS Catalina

    The next OS release for the Mac will arrive during September. macOS Catalina is a major OS release and includes many new features.

    As usual our developers have been hard at work ensuring that when macOS Catalina is released, MacVector 17 will be fully compatible.

    For older versions you can check compatibility on our website as soon as macOS Catalina is officially released.

    For versions of MacVector released over the past few years it is likely that they will work fine. For these we have been striving to future proof MacVector for new versions of macOS.

    However, for older versions of MacVector there will be issues. More significantly MacVector 13.5 and all older versions will not run. The MacVector application icon will be displayed with a “stop sign” indicating it will not run.

    This is due to Apple moving fully to a 64 bit operating system.

    Starting with the release of macOS High Sierra 10.13.4 any 32 bit application would periodically display warning dialogs. For example: “the application is not optimised for this release and needs to be updated” and “This application will not work on future macOS releases”. However, the application would still run. But with the release of macOS Catalina this migration is now complete and 32bit applications will no longer run.

    Here at MacVector we always strive to stay ahead of the game. When Apple recommended (many years ago) that all applications should be 64 bit, we immediately started working to move MacVector to be fully 64 bit resulting in the release of MacVector 14 in 2015.

    Please do note that whereas our developers do develop and run MacVector on Apple’s public and developer betas of macOS, we really do not recommend that users run MacVector for any real workflows on beta releases. There may be unexpected issues that you may encounter.

    Posted in Releases | Tagged , | Comments closed

    Upgrade to the most feature packed version of MacVector yet and install on multiple Macs with a 50% discount.

    Personal licenses are ideal for using on a single Mac, but not if you have multiple Macs or want to install on a shared lab computer as well as your personal Mac. So why not upgrade to a standard license of MacVector Pro 17 that you can share among a group of users in the same research group?

    What’s even more flexible is if you take your laptop home, or away on travel to a conference, then you can work on MacVector and the license back in the lab will still work!

    During August we have a 50% discount on either exchanging a current personal license to a standard license, or upgrading an older personal license to a standard one of MacVector 17.

    MacVector 17 is one of the most feature-packed updates that we have ever released. Highlights include an interactive Restriction Enzyme Picker, a unique genome comparison tool and a tool to help you design and document Gibson Assembly and LIC workflows. MacVector 17 has support for Dark Mode, helps identify genome sequencing errors, automatically displays primer binding sites, maps multiple sequencing datasets against a single reference and has numerous performance improvements.

    How to upgrade a personal license to a standard license.

    Personal Licenses are locked to a single Mac. They are best suited to a single person using MacVector.

    Standard licenses may be installed on ALL Macs in a lab with one concurrent user. Standard licenses use Bonjour to check if the serial number is in use. If there is no network they just work.

    To upgrade request a quote or email for more information.

    Posted in Releases | Tagged | Comments closed

    The MacVector Team will be at ASM Microbe 2019 in San Francisco.

    We’re at ASM Microbe 2019 in San Francisco from Friday 21st June until Sunday 23rd.

    The show is finally back on the West Coast at the Moscone Convention Center after 6 years on the East Coast and New Orleans.

    This year the exhibit hall hours are unchanged from last year’s show:

  • Friday, June 21st – 10:30 AM – 5:00 PM
  • Sat. June 22nd – 10:30 AM – 5:00 PM
  • Sunday, June 23rd – 10:00 AM – 4:00 PM
  • We’re on booth 1731.

    Please do drop by. We’ll be demoing our latest release, MacVector 17.

    If you’ve never used MacVector before, or you are a power user, then please drop by and say hello. We always enjoy meeting users and we guarantee we can teach you something new, and hopefully you’ll be able to teach us something new too!

    See you in San Francisco!

    The Twitter hashtag looks to be #ASMMICROBE2019.

    Posted in General, Meetings | Tagged | Comments closed

    What can MacVector do for my lab?

    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.

    Compare Genomes: Compares two related annotated genomes to identify identical, similar and weakly similar features.

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

    Coverage Tab: Compare different datasets assembled against the same reference sequence with expression level comparison.

    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

    How Do I?: new menu shows common workflows with step by step guides. Every tool has a link to a video tutorial.

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

    Restriction Enzyme Picker: easy identification of useful enzyme cut sites.

    Cloning

    Gibson/Ligase-Independent Assemblies: Automatic primer design and assembly for Gibson Assembly or Ligase Independent Cloning workflows.

    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.

    Scan For… Missing Primers: utilize the power of the Primer Database to display binding sites from your lab’s primer collection

    Read More…

    Posted in Releases | Tagged , , , | Comments closed

    HOW DO I video guides to common molecular biology workflows

    MacVector has a wide array of different tools for working with protein and DNA sequences. MacVector has always been designed with the Mac’s simplicity in mind and getting started with simple tasks is quick. However, making the most of the many functions and getting familiar with MacVector’s wide range of tools does require more help

    Nobody has time to read manuals nowadays and so with that in mind we set out to try to help new users get up to speed quicker and help more advanced users know tools they may not be that familiar with.

    MacVector 17 introduces a new menu which lists common workflows that a molecular biologist may need. Each topic has a short video and/or a short step by step guides. What’s more is every tool’s dialog now has a link to a video tutorial.

    So if you need to know how to do something then try the HOW DO I menu.

    If you need to know more about a tool then click the (?) button in every dialog.HOWDOI IndexHOWDOI MENU

    Posted in Tips | Tagged | Comments closed

    Show or hide the RE Picker and the Graphics Palette from the toolbar

    MacVector 17’s brand new Restriction Enzyme Picker gives you an interactive way to quickly show what enzymes will digest your sequence. You can dynamically filter what sites are displayed. For example to show just 3’ overhang cutters or use other criteria. What’s more is that you can take a set of cut sites from one sequence (for example an expression vector) as the input to digests of other sequences for easier optimizing of construct workflows.

    However, along with the Cloning Clipboard and the Graphics Palette you might find your screen has the dreaded window clutter. So we’ve added two new toolbar buttons to very quickly show or hide the floating tools.

    REPicker toolbarButtons

    A few users with customized window preferences may not see these by default. If this includes you, right-click (or [ctrl]-click) on the toolbar and choose Customize Toolbar in the popup menu. Drag the two buttons to your toolbar, or drag the default set of toolbar buttons.

    Image002

    Posted in Tips | Tagged , , , | Comments closed

    MacVector 17: Our most feature packed release yet..

    MacVector 17 will be released later this week.

    Get ready for our biggest release yet. MacVector 17 compares genomes, makes restriction enzyme cloning easier, automates the design of Gibson Assembly and Ligase Independent Cloning strategies. Makes plasmid maps even more beautiful and supports macOS Mojave’s Dark Mode to aid concentration on those late night primer design sessions!

    For sequence assembly there’s a stack of new features. Align to Folder has a new Assembly Problems tab that identifies possible issues with your assembly (and what to do about them). For reference assemblies in Assembler there’s a new Coverage tab that allows you to compare multiple assemblies when mapped against the same reference. For example you can compare different sequencing datasets from different samples, the same dataset mapped with different parameters, or compare RNAseq datasets.

    For cloning the new Restriction Enzyme Picker gives you an interactive way to quickly show what enzymes will digest your sequence. The new floating tool initially presents you with a list of all available sites in a sequence. However, you can filter on many attributes, such as number of cuts, 5’ or 3’ overhangs and blunt ends. What’s more is that you can take a set of cut sites from one sequence (for example an expression vector) as the input to digests of other sequences for easier optimizing of construct workflows.

    For non restriction enzyme based cloning the new Gibson Assembly/Ligase Independent Cloning tool provides automated design of ligase-independent cloning strategies. The tool supports 5’ exonuclease driven Gibson assembly as well as the T4 DNA Polymerase 3’ exonuclease “Ligase Independent Cloning” approach. It can automatically design primers when you specify fragments and vectors to use. Alternatively you can provide custom primers (manually or from tools such as the NEBuilder website). You can also just provide existing fragments with overlapping ends for MacVector to assemble. The interface shows the exact structure of the junctions between fragments, including relevant CDS translations for confirming the frame of protein fusions. The cloning strategy can be saved as a new cloning project document and finally automatically assembled into a single sequence.

    Over the past few releases many new tools and features have been added to make fully annotated and beautiful plasmid map’s easier than ever. Continuing this theme MacVector 17 now utilises the power of the Primer Database and will automatically display your very own freezer drawer collection of oligos directly on your sequence, automatically! That means when you open even blank unannotated sequences you will see common features, RE recognition sites, putative ORFs and now your primer binding sites.

    Scan for.. Missing Primers joins the existing Scan for tools that automatically display restriction sites, missing common features and putative open reading frames on your sequences.

    This release is also aimed at making life easier for new users. There’s a brand new How Do I menu that shows common workflows with either simple step by step guides, or short videos. Plus every tool now has a link to a help topic on how to use it. MacVector has always been easy to use, but now even the most complicated tool has a simple way to get started… Quickly!

    Finally we’re excited to announce that MacVector 17 supports macOS Mojave’s Dark Mode. When you are working late at night designing those constructs, then Dark Mode will help aid your concentration!

    Here’s a full list of what’s new in MacVector 17

    There’s also a more detailed list and the Release Notes.

    Dark Mode Support: use macOS Mojave’s Dark Mode to aid concentration on those late night primer design sessions!

    Scan For… Missing Primers: utilize the power of the Primer Database to display binding sites from your lab primer collection

    Restriction Enzyme Picker: a new tool for easy identification of useful enzyme cut sites. Dynamically filter Restriction Enzymes to simplify the identification of useful enzyme cut sites. Use cut sites from one sequence as the input to others for planning construct workflows.

    Compare Genomes: Compares two related annotated genomes to identify and list identical, similar and weakly similar features along with missing features.

    Gibson/Ligase-Independent Assemblies: Automatic primer design and assembly for Gibson Cloning or Ligase Independent Cloning methods.

    MacVector

    How Do I?: new menu shows common workflows with step by step guides. Every tool has a link to a video tutorial.

    Assembly Problems: identify mis-assembled sequences based on excessive mismatches, discontinuous reads and other common problems.

    Coverage Tab: Compare different datasets assembled against the same reference sequence with expression level comparison.

    Redesigned Assembly Project: Easier organization of multiple datasets, multiple reference sequences and repeated jobs.

    How to upgrade to MacVector 17.0

    If you have active maintenance and are running MacVector 15.5.4 or later then you will be notified about the new release. To install this version, you must have a maintenance contract that was active on 1st November, 2018. You must also be running MacVector 15.5.4 and OS X 10.9 Mavericks or later.

    If you have an older version of MacVector then download the trial and request an upgrade quote.

    Even if you have downloaded the trial in the past then downloading a new trial will give you a fresh 21 days to evaluate MacVector.

    When a trial license expires it becomes MacVector Free. So if you decide against upgrading then you can just delete the trial license and easily go back to your current version. It’s risk free as MacVector files are backwards compatible.

    Posted in Releases | Tagged | Comments closed