Thanks to everyone who responded (Mark Schonewille, Mark Smith, Viktoras Didziulis, Robert Brenstein, apologies if I forgot anyone) - a whole range of solutions, including arrays, databases and 'just' variables. Anyway, I coded up the brute force method without any finess... here's the business bit of the script with some frippery...
global seqDB ON mouseUp put the number of lines in field "massList" into peptides put "Processing " & peptides & " masses, please wait..." into field "Output" put the long time into field "Start" put empty into outputData set the tabstops of field "Output" to 120, 390, 10,20 put field "ppm" into ppm REPEAT for each line pepMass in field "massList" put "NEW SEARCH, MASS = " & pepMass & " at " & ppm & " ppm error" & return after outputData put pepMass * ppm/1000000 into massError REPEAT for each line peptide in seqDB put the third word of peptide into dbMass IF abs(pepMass-dbMass) <= massError THEN put peptide & "K" & tab & dbMass-pepMass & return after outputData END REPEAT put "====================" & return after outputData END REPEAT put outputData into field "Output" put the long time into field "Stop" END mouseUp I ran a brutal test, of 45,000 lines in massList and 16,000 lines in seqDB My crude attempt seems to be capable, even running within the Rev IDE, of completing the 720million comparisons in about 30minutes (OK, admittedly CoreDuo 2.66GHz, 2GB RAM). That's 24million a minute! (I deliberately put some searches that would match at the end of seqDB, to be sure I searched through most of the file each time). I am pretty happy with this, and I'd be looking for at least a 10-fold gain in speed to code up a harder solution. Do you experts thing a 10-fold gain is feasible? 100-fold? Rob ________________________________ Prof R J Beynon[h] Proteomics and Functional Genomics Group Faculty of Veterinary Science University of Liverpool Crown Street, Liverpool L69 7ZJ ________________________________ Phone: +44 151 794 4312 Fax: +44 151 794 4243 Email: [EMAIL PROTECTED] http://www.liv.ac.uk/pfg ________________________________ This email was sent on Sun, 15 Jul, 2007 at 8:58 PM. _______________________________________________ use-revolution mailing list use-revolution@lists.runrev.com Please visit this url to subscribe, unsubscribe and manage your subscription preferences: http://lists.runrev.com/mailman/listinfo/use-revolution