Note: Make sure that you have enabled search based alerts SSP-> Search Settings -> Search Based Alerts

   1: SPSite spSite = new SPSite("http://nishand:300/sites/PubSite/Search/");

   2: SPWeb web = spSite.OpenWeb();

   3: Query alertQuery = new KeywordQuery(spSite);

   4: alertQuery.QueryText = "Hello" // Keyword

   5: SearchAlert searchAlert = new SearchAlert(spSite, alertQuery); 

   6: searchAlert.InnerAlert.AlertFrequency = SPAlertFrequency.Daily; 

   7: searchAlert.InnerAlert.Title = "Alert#2"

   8: searchAlert.InnerAlert.User = web.Users["domain\\user"]; 

   9: searchAlert.Update();

How to check whether an alert named 'Alert#2' has been created?

  Go to Site Actions ->  Site Settings - User Alerts -> Select 'user name' and click on 'update' button.