It is possible to search individual sequence documents not only for text occurrences but by similarity to sequence fragments. Open the Advanced Search (see Fig 4.2 ) , 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 16 . The search does not work on sequence lists, alignment/assembly or tree documents.
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.
It is also possible to sort individual sequences documents in a given folder by their similarity. To use this function, select a single sequence in the document table and right-click, then choose Sort. Sort by similarity will rank all other sequences by their similarity to the selected sequence. The most similar sequence is placed at the top and the least similar sequence at the bottom. This also produces an E-value column describing how similar the sequences are to the selected one. The Remove Sort by Similarity option will remove the E-value column and return the table to its previous sorting.