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 approach to performance tuning has ensured this release of MacVector is faster than ever.
With our new online updating tool updating to MacVector 13.5 is easy too!
The graphics Symbol Editor and floating Graphics Palette have been rewritten in preparation for MacVector moving to a 64-bit architecture (due with MacVector 14.0). The other main enhancements have been aimed at better handling of Next Generation Sequencing (NGS) files, particularly with the Align To Folder and Assembler Velvet de novo assembly functionality. There has also been some code optimization to better handle the analysis of large genomic sequences, particularly noticeable with the Pustell Matrix “dot-plot” functionality.
Align To Reference Enhancements
Align To Reference now handles alignments around a circular sequence. Note that this is only the case for the “Sequence Confirmation” algorithm. The cDNA Alignment algorithm still assumes the target sequence is linear.
You can now select one or more sequence “Reads” in the Align To Reference Editor and save those reads to a fasta or fastq formatted file by choosing File | Export… and selecting the required format in the resulting dialog. In particular, this lets you run alignments of up to 500,000 NGS reads against a reference sequence and then specifically export all of the aligned (or non-aligned) reads for further analysis.
The cDNA Align To Reference algorithm now does a much better job of displaying segmented reads in the Map view.
Align To Folder Enhancements
Align To Folder can now perform alignments against fasta and fastq files with many millions of reads.
You can now retrieve the “hits” from an Align To Folder run to one of three destinations – the MacVector Desktop (i.e. opening each hit in a window on the screen), to a folder (where each hit is written out as a separate file) or to a single file (where the hits are concatenated into a single fasta or fastq file).
Taken together, these enhancements let you use Align To Folder to pull out rare matching reads from large NGS datasets for use in further analysis or DNA Assembly. In beta testing, this has been used to “clone” genes from MiSeq RNA-Seq runs using Protein source sequences aligned to Fastq data.
Pustell Matrix (“Dot Plot”) Enhancements
The performance of large (i.e. genome-sized) Pustell Matrix dot plot alignments has been dramatically improved. You can now scan and display pairs of bacterial genomes in just a few seconds to easily identify inversions, duplications and rearrangements in their gene organization. You can zoom in and out of the dot plot display in real time to explore the relationships right down to the residue level.
Nucleic Acid Subsequence Enhancements
A small but significant change has been made to the graphical output of this. If you select a pair of hits in the Map results tab, then choose Edit | Copy, the sequences of the actual subsequences are substituted into the copied sequence. This allows you to maintain primers in a nucleic acid subsequence file and use the Nucleic Acid Subsequence analysis option to quickly identify and “clone” predicted PCR fragments even if the primers have mismatches or tails added to them.
Assembler Enhancements
Reference alignments (from Bowtie) now have a separate coverage report tab that lists the read coverage for every gene and CDS feature in the reference sequence. You can use this to (e.g.) accurately measure relative expression levels of mRNA in RNA-Seq experiments or plasmid copy number in whole cell DNA sequencing experiments.
Velvet now does a much better job at trimming poor quality residues from input sequences.
Velvet now handles paired sequences that have identical names.
You can now export unassembled reads from Bowtie and Velvet alignments as fasta or fastq files. This lets you filter out reads that match specific sequences so you can focus subsequent alignments using a subset of reads.
Miscellaneous Enhancements
You can now reset the circular origin of circular sequences to any arbitrary position. Simply click between the residues where you want the new origin to be, then right-click (or -click) and choose Set Circular Origin from the popup menu.
Informative tooltips have been restored in all views.
A number of issues with saving trace files have been resolved. In particular, you can now use the bsml format to save annotations with chromatogram information.
We’ve worked hard to bring you this release and we really hope that it makes your day in the lab just that bit easier!
If you have not yet updated to MacVector 13.5 then all you need to do is:
– Open MacVector
– click on MACVECTOR > CHECK FOR UPDATES…
If you do not have a license then do not miss out. Download the trial now.
