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!

Know Your Alignments

We often get asked “how do I do an alignment” using MacVector? Well, the answer to that is always “it depends”, and it depends on what you want to learn about your sequence(s). Here’s a quick summary of the different types of alignments and what you would use them for:

  • Multiple Sequence Alignment (File | New | Protein Alignment or Analyze | Align Multiple Sequences Using | …) Use this when you want to explore the relationships between sequences. This is primarily aimed at protein sequences. Unless you want to explore the phylogenetic relationship between nucleic acid sequences (e.g. rRNA) there are almost always better approaches to use for DNA sequences.
  • Align To Reference (Analyze | Align To Reference). If you are working with DNA sequences, this should be the first function you consider for alignments. Use this to align one or more nucleic acid sequences against a reference. It handles regular sequences, ABI chromatogram files and even NGS data. This is the ideal interface for resequencing and mutagenesis identification experiments. The algorithm is strand aware enough to automatically “flip” sequences as appropriate and can even align cDNA sequences to a genome, accounting for introns and splice sites.
  • Dot Plots (Analyze | Create Dot Plot | …). This is a great and underrated function for quickly comparing 2 sequences to get an overview of the similarity between them. You can use this to quickly check that two sequences do have some similarity, but you can also use it to compare two genomes and see were the identities, duplications and inversions are located. This is also a good way to see the extent of local alignments between two sequences.
  • BLAST. (Database | Internet BLAST Search). MacVector’s implementation of the standard NCBI BLAST search. But still a great way of getting a quick idea of which sequences your sample is related to.
  • Align To Folder. (Database | Align To Folder). Like BLAST, but for your own personal sequences. Handles fasta and fastq files so that you can use this to pick out reads from a huge database that match your sample sequence.
  • Primer Database. (Analyze | Primer Database Search). A relatively new addition to MacVector, but you can use this to align a collection of primers to a test sequence. This lets you define tails for your primers and you can even select a pair of primers in the graphical result window and Edit | Copy will copy the predicted amplification product, complete with any engineered mismatches and overhanging tails.
  • You can learn more about the different alignment options in these three blog posts, Alignments in MacVector, Aligning Trace files, and Aligning primers to a Reference sequence.

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