Hi Ali, Greg made some good comments on your post regarding the Sequest search engine. I'm curious as to what search engine you're using. The TPP includes X!Tandem, which is generally significantly faster than Sequest, and is multi-threaded (and free, so you can even consider running it across a cluster-- something we're hoping to make easier in the future). Note, though, all search engines, including X!Tandem, are affected by the search parameters that you use. So a semi-tryptic search will generally always take longer than a full-tryptic search but increase the search space (which is good), so it's always going to be a trade-off. We include some default X!Tandem parameter files; as you get more experience, you might want to play with modifying some of the parameters to optimize your search.
Natalie On Fri, Jul 10, 2009 at 6:59 AM, Greg Bowersock <[email protected]> wrote: > Sequest is not very fast. The only way to really speed up sequest is to > give it more processors, provided you are using sequest in a way that will > allow you to use the extra processors. There are many factors that affect > the speed of processing though, with the two largest being the type of > digestion and the size of the database. The number of modifications also > plays a role in the amount of time, so as you can see there isn't any one > way to really speed up sequest. Also, 10 hours isn't all that bad, try doing > a no-enzyme search on a decent sized database, that can take days on 1-2 > processors. > > > On Fri, Jul 10, 2009 at 4:42 AM, Ali <[email protected]> wrote: > >> >> Hi everyone >> >> I am doing some databse search with mzXML files generated from >> Thermo .raw files against my database. I have a duo core 2GB RAM >> machine. I understand that TPP does not use multi-threading but one >> mzXML file seems to take 10 hours to process!! Is there anyway I can >> speed up this process? >> >> Regards >> >> Ali >> >> >> --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
