For analysing large sequencing datasets, whether de novo or mapping reads against a reference 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:
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 such as a plasmid too.
