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

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 add new tools, and redesign old ones, to keep ahead of new trends in the molecular biology lab.

This results in multiple releases every year as well as many minor bug fix releases. As a small company, we are agile and able to respond to bug reports very quickly. As far as software development goes, bigger is not always better.

Here’s a short review of what we did last year and what is on our “to do” list for this year. We hope you find this useful and informative.

The MacVector team.

2014 Review:

There were two major releases of MacVector in 2014: MacVector 13 at the beginning of the year and MacVector 13.5 towards the end.

As well as the more visible new tools, a lot of small enhancements and a great deal of under the hood work was completed last year. The Mavericks and Yosemite OS X releases introduced a lot of changes, not least the new muted flat look, and we ensured MacVector remained fully compatible and redesigned the toolbar icons to complement that look. The redesign and rewrite of the old style results windows was completed and general performance tuning ensured the last release of 2014 was the fastest yet.

Our Quicktest Primers tool was enhanced to show restriction enzyme sites around the binding site of the primer. Potential “one-out” sites are shown and are colored to show whether they will affect encoded protein sequences.

Velvet was added to Assembler for de novo assembly of NGS data. Reference assemblies show the read coverage of every CDS and gene for comparison of expression levels across samples for RNA-Seq and ChIP-Seq.

The performance of the Align to Reference and Align to Folder algorithms was enhanced and you can retrieve and/or export hits in Align to Folder. These enhancements allow easier processing of NGS reads if you are just analyzing a single gene.

What’s coming in 2015?

During 2015 there will be multiple releases. The first release will be MacVector 14 and is very significant as it will be a fully 64 bit application. This has performance advantages when run on modern Macs, particularly the ability to handle longer sequences, larger alignments and bigger fastq files. MacVector’s rich graphics view is great for viewing your sequences and with MacVector 14 it will be optimized even for chromosome sized sequences.

We are very excited about this release and also for what this means for future releases. The transition to 64 bit is the cumulation of a lot of hard work behind the scenes that has gone into development over the past few years. Being a 64 bit application means MacVector will be better able to exploit the larger RAM capacities of modern Macs. This mean smoother and more responsive graphics, faster algorithms and many limitations, when working with very large datasets, will be gone. We are sure that you will be excited to see the levels of performance that you will see on your desktop!

Other new features in the 2015 releases will include:

  • Protein annotation: You’ll be able to scan sequences against InterProScan, which has a wide variety of protein sequence, protein families, domains and motifs databases.
  • Primer Database: All primer tools will now connect to a database of primers. You will be able to scan sequences against the database to quickly identify binding sites for your primers (available in MacVector 14).
  • Applescript support will be added for Auto-Annotate. Do you’ll be able to batch annotate folders of blank sequences using a curated library of sequences.
  • Assembler: the focus will again be on better visualization of your assembly results. You will have expression level comparison across contigs from separate samples.
  • Lastly, 2015 will see a solution for those users who only need a straightforward sequence analysis application to design primers and clone genes. A new edition of MacVector will fill the needs of these researchers.

    At MacVector we greatly appreciate hearing from users on what they want to see, so we always encourage you to keep us updated on your needs and what you need in a sequence analysis application. As always, our mission is to keep MacVector the easiest to use and best sequence analysis application for the Mac.

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