When Sequest runs in Bioworks it will index the sequence database at the beginning of the search. If you have at least 1G of RAM (there is a database size limitation but I can't remember) you should be able to use this feature from the command line with the -I+ argument. Execute sequest.exe -HA to get more information. Also you can use the database tools in Bioworks Browser to create indexed databases on your disk. Bill
On Feb 21, 9:04 am, David Chiang <da...@sagenresearch.com> wrote: > FYI - Our company makes the SORCERER 2 integrated data appliance > system with a fast SEQUEST and integrated TPP as the standard > workflow. Currently, our version of SEQUEST (rewrote from scratch for > servers) runs on 8 CPU cores, and can generally process 10,000 spectra > with 3 variable mods in less than 30 minutes for single-species > protein sequences. > > Not trying to make a sales pitch here, but wanted to let you know such > a system exists, and that we've shipped about 70 SORCERER systems to > the field over 4 years to many top labs. > > Anyway, I've posted these blog entries if you're interested in how our > system works, and why many big labs use SEQUEST as the main engine for > TPP despite it's compute-intensive (ie expensive) nature: > 1) http://proteomics2.com/?p=69 (How SORCERER works) > 2) http://proteomics2.com/?p=86 (Why SEQUEST with TPP for really > big data sets) > > Many people see the search engines as being equivalent and > interchangeable, which is not true when you are trying to get the > absolute best sensitivity possible. > > Anyway, hope these help to get everyone thinking more deeply and > asking more questions about how to accelerate the whole field forward. > > Sincerely, David Chiang (Sage-N Research) --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
