4.2.2 Similarity (“BLAST-like”) searching

It is possible to search your local documents not only for text occurrences but by similarity to sequence fragments. Click the small arrow at the bottom of the large T to the left of the search dialog, select Nucleotide similarity search or Protein similarity search and enter the sequence text. Geneious will try to guess the type of search based on the text, so that simply entering or pasting a sequence fragment may change the search type automatically.

The search locates documents containing a similar string of residues, and orders them in decreasing order of similarity to the string. The ordering is based on calculating an E-value for each match. You can read more about the E-value in chapter 15 .

For the search to be successful, you need to specify a minimum of 11 nucleotides and 3 amino acids. Note that search times depend on the number and size of your sequence documents, and so may take a long time to complete.