Tag: alignments

  • Use dot plots to quickly confirm similarity between two sequences

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    Chris
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    We occasionally get e-mails from users who think that two sequences should align using ClustalW or the Align To Reference function, but the algorithms cannot find any meaningful matches. In these cases, the first thing I do is open both sequences and then create a dot-plot between them using the Analyze | Create Dotplot |…

  • How to remove gaps from a sequence

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    Chris
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    There are often times when you end up with a sequence containing gaps, especially if you make extensive use of the Align To Reference, Contig Assembly or Multiple Sequence Alignment interfaces to generate consensus sequences. You can select and copy the consensus sequence, or even individual aligned reads, from the Align To Reference and Contig…

  • Use Analyze -> Align To Reference to align ABI trace files

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    Chris
    in

    One of the most common tasks in any molecular biology lab is the need to re-sequence a piece of DNA. Perhaps it is a cloned PCR fragment where you want to confirm the sequence, perhaps you are sequencing across a cloning junction, or maybe screening clones for a successful mutagenesis experiment. Many users immediately think…

  • 101 things you (maybe) didn’t know about MacVector: #45 – Automatically annotating sequences using BLAST

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    Kevin
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    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…

  • Quickly checking a small sequencing project

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    Chris
    in ,

    For analysing large sequencing datasets, whether de novo or mapping reads against a reference you need Assembler. However, many times you do not need a powerful tool but just a quick way to check some sequencing data. For example for checking small sequencing projects, such as a site directed mutagenesis, looking for SNPs in a…

  • MacVector Talk: January 2015: A review of 2014 and what’s coming in 2015.

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    Chris
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    MacVector and Assembler: What’s Next! We strive to make MacVector the best sequence analysis app for the Mac. This means our developers are continually at work redesigning every aspect of MacVector, not only to improve functionality, but also to ensure that MacVector is always optimized for the latest versions of OS X. In addition we…

  • MacVector 13.5 is out

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    Chris
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    MacVector 13.5 was released last week. MacVector 13.5 is the best release yet. It’s had a redesign and rewrite of existing tools to make comparing large sequences faster and to improve handling of NGS data. Additionally the new interface, introduced in MacVector 13.0, has had many “tweaks” in response to user feedback. Plus a continued…

  • MacVector 12.7 is now out.

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    Chris
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    We’re pleased to announce that MacVector 12.7 has just been released. The most exciting new feature is the Cloning Clipboard. We’ve had a lot of user requests over the past few years for help with designing cloning operations and the user feedback we had during the beta testing of MacVector 12.7 makes us think we’ve…