The blue logo of MacVector, inc.

Tag: weeklytip

  • Assemble bacterial genomes in minutes on your Mac laptop

    —

    by

    Chris
    in

    MacVector with Assembler contains some remarkably powerful algorithms for assembling Next Generation Sequencing (NGS) data. Not so long ago, you needed a powerful Linux server with lots of memory for de novo assembly of whole genomes. But with advances in the efficiency of algorithms and improvements in hardware, it is now possible to assemble quite…

  • Simple Assembly of Sanger Sequencing Files with MacVector Assembler

    —

    by

    Chris
    in

    Update: As of September 2024 Assembler will be added at no cost when you upgrade or renew maintenance. Contact Support if you have not yet been upgraded. With MacVector Assembler, assembling ABI Sanger Sequencing files is simple, fast and accurate. MacVector uses the popular phred/phrap/cross_match set of tools from the University of Washington. To improve…

  • Use the Replica Button For Synchronized Views

    —

    by

    Chris
    in

    Most primary MacVector windows (Nucleic Acid Sequence, Protein Sequence, Multiple Sequence Alignment, Align To Reference, Contig Assembly etc.) have a Replica toolbar button. If you click that button, a second window will open, potentially set to a different tab. The key to this functionality is that the two windows are linked – any selections you…

  • How to Identify Bacterial Promoters Using MacVector

    —

    by

    Chris
    in

    MacVector’s Subsequence tool is a very flexible search function that can be used for a variety of tasks. MacVector itself has a built-in variant of the function for maintaining and search primer databases (Analyze | Primer Database Search…). Each entry in the file MacVector uses as a source of subsequence data can have up to…

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

    —

    by

    Chris
    in

    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…

  • Opening multiple sequences as alignments or individual sequences

    —

    by

    Chris
    in

    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.…

  • RNASeq Expression Analysis with NGS data

    —

    by

    Chris
    in

    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…

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

    —

    by

    Chris
    in ,

    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…

  • Downloading hits from the MacVector BLAST Map results tab

    —

    by

    Chris
    in

    MacVector’s BLAST Map results tab (added in MacVector 15.5) is a unique interface for examining the annotations around hits to a query sequence. Each pane in the display represents a High Scoring Segment Pair, as seen in the BLAST Aligned Sequence tab. At the lower left corner of each pane is a Download button –…

  • Controlling The Automatic ORF Display in MacVector 15.5

    —

    by

    Chris
    in

    MacVector automatically scans every DNA sequence window for open reading frames and displays the results in the Map tab. The setting for this are controlled by the MacVector | Preferences -> DNA Map pane, along with the automatic Show restriction sites settings. The Minimum Number of Codons setting is fairly obvious. 5’ ends are starts…