> So, ok 67+25=92 seconds is not real impressive compared to 17, and I'm not > sure how > much I can blame cygwin for this :) I guess once I'm sure I have a useful > algorithm, > I can subtract IO time which has been significant in many cases.
I wasn't going to bother to look given the time differences are> 4x but I did note they tested on a 3Ghz Pentium 4 and I have something that comes up as "x86 Family 6 Model 8 Stepping 3" which is probably ca. 1 Ghz ( I never bothered to check since I thought a 2-3x factor wasn't important). I guess by the time you subtract IO it may be pretty close. It would be hard to blame cygwin for the computational time however :) > From: [EMAIL PROTECTED] > To: [email protected]; [EMAIL PROTECTED] > Date: Tue, 19 Feb 2008 11:51:39 -0500 > Subject: Re: [BiO BB] Need fair alignment tool comparison/ using DSCAM for > tool testing > > >> We have been using MUMmer3 (http://mummer.sourceforge.net) for rapid >> alignments of whole genomes, genomes and contigs, and searching for > > Thanks- that looks like a good tool that I didn't know about. I noticed they > advertize e coli results > prompting me to go back and check my own. I'd have to go check the suffix > tree literature > to see what exactly they claim to do in 17 seconds on e coli, but under > cygwin, I was able to > index all matching strings of length 25 or more, in about 67 seconds , > > $ date;$progpath/string_test -fastas both_fasta -index 8 -length 25 -fix 12 > -output 3 -filterN -filterID -status -fcompare_all> anchors ;date > Sat Nov 10 18:45:23 EST 2007 > string_test.cpp177 loaded 2 fastas > Sat Nov 10 18:46:30 EST 2007 > > > and create a coarse alignment in another 25 seconds, > > $ date; $progpath/mm_align_tool -fastas both_fasta -v -pair_rules anchors > -doall -pair_align 0 -output text> align1 ;date > Sat Nov 10 18:50:01 EST 2007 > mm_hit_classes.h389 > annotation_model.h57 Loaded 33373 pair rules. > mm_align_tool.cpp309 Doing string PAIR align with cutoff 3 > mm_align_tool.h227 do_all with only one rule, did you mean -mrules? > mm_align_tool.cpp318 doing 0 vs 1 > mm_align_tool.cpp326 do hit dump rules > Sat Nov 10 18:50:26 EST 2007 > > > Do you have actual timing tests for various complete tasks or is 17 seconds > about it? > So, ok 67+25=92 seconds is not real impressive compared to 17, and I'm not > sure how > much I can blame cygwin for this :) I guess once I'm sure I have a useful > algorithm, > I can subtract IO time which has been significant in many cases. > Someone also privately suggested blast's bl2seq and I would point out that > this is quite fast on pairs > of 50k sequences. > > > > > Mike Marchywka > 586 Saint James Walk > Marietta GA 30067-7165 > 404-788-1216 (C)<- leave message > 989-348-4796 (P)<- emergency only > [EMAIL PROTECTED] > Note: Hotmail is blocking my mom's entire > ISP claiming it is to reduce spam but probably > to force users to use hotmail. Please DON'T > assume I am ignoring you and try > me on [EMAIL PROTECTED] if no reply > here. Thanks. > > > _________________________________________________________________ > Shed those extra pounds with MSN and The Biggest Loser! > http://biggestloser.msn.com/ > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Helping your favorite cause is as easy as instant messaging. You IM, we give. http://im.live.com/Messenger/IM/Home/?source=text_hotmail_join _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
