Tag: weeklytip

  • Opening multiple sequences as alignments or individual sequences

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    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

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    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

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    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

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    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

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    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…

  • Use the BLAST Map to better identify blast hits

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    by

    Chris
    in

    With the advent of cheap Next Generation Sequencing technologies, there has been an explosion of whole genome sequences deposited in BLAST databases. One consequence of this is that, particularly for sequences of bacterial origin, most of the significant hits are to entire genomes. The classic BLAST results show the sequence alignments, but give no indication…

  • Downloading hits from the MacVector 15.5 BLAST Map results tab

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    by

    Chris
    in

    The MacVector 15.5 BLAST Map results tab 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 – when you…

  • Controlling Automatic ORF Display

    —

    by

    Chris
    in

    MacVector 15.5 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…

  • Use the BLAST Map to better identify blast hits

    —

    by

    Chris
    in ,

    With the advent of cheap Next Generation Sequencing technologies, there has been an explosion of whole genome sequences deposited in BLAST databases. One consequence of this is that, particularly for sequences of bacterial origin, most of the significant hits are to entire genomes. The classic BLAST results show the sequence alignments, but give no indication…

  • Generating a primer report to send to your Oligo Synthesis service

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    by

    Chris
    in

    QuickTest Primer is a great tool for primer design. Paired with Primer Design/Test (Pairs) it gives you great control and flexibility for designing primers with tails, mismatches, silent mutations, one out sites and more. Once you’ve designed your primer the next step is to get it synthesized. QuickTest Primer will produce a PDF report of…