General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Quickly checking a small sequencing project

For analyzing large sequencing datasets 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 PCR product, cloning a gene or checking your latest construct is correct. MacVector has a built in tool called ALIGN TO REFERENCE that’s specifically designed for such tasks.

The tool is capable of quite complex workflows, including aligning mRNA and EST data against genomic references. However, for checking your latest construct the steps are pretty simple:

  • Open up your reference.
  • ANALYZE | ALIGN TO REFERENCE
  • In the new window click ADD SEQS and add your reads or trace files.
  • Click ALIGN and choose SEQUENCE CONFIRMATION
  • Choose the defaults and click OK.
  • The reads will be aligned against the reference and show a consensus. Reads are automatically reverse complemented if needed.

    Click on the DOTS button to hide all bases that match the consensus, and only show mismatches. There’s also the MAP tab that shows a graphical view of all reads and the reference. You can align against a circular reference too!

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