We are going to do the same search that we performed with BLAST and Fasta, with the Felis catus cannabinoid receptor 1, to see how similar the results are to those that with got with the previous searches.

Paste your sequence into the main text-entry box in the Smith-Waterman home page at EBI. We shall select the Swissprot protein database against which to perform our search. We can leave the default settings for the moment. Be sure to change the database that we are searching against to Swissprot. Also change the Program type from Normal to Affine to allow the use of affine gap penalties (i.e., gap extension penalties are a fraction of the penalty to open a gap). Click 'Run'.

Our results will appear in the same window shortly. As with FASTA, the sequence is not filtered for low complexity regions.

The main results page contains a summary table, similar to the FASTA result page. Note the affine gap penalties.

The 'MPsrch Result' button takes you to a page which details the parameters of this run (again, similarly to the FASTA results page). From the text at the top of this file, we can again notice that the Swissprot database that is used in the Smith-Waterman searches is different from both the one used by NCBI and the one used by the FASTA search.

However, the results that we get are very similar to those that we get doing the FASTA search. The layout is slightly different. And, as in BLAST, only the portions of the sequence that are actually involved in the match are shown.