[BiO BB] Need fair alignment tool comparison/ using DSCAM for tool testing

[Mike Marchywka]

> 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.




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