[Bioclusters] quick look see at fractal computing.

James Cuff jcuff at broad.mit.edu
Thu Mar 2 18:17:50 EST 2006

On Thu, 2 Mar 2006, Nick Robertson wrote:

> It is still unclear to me why your results are markedly different
> from NCBI and MPT, but it's probably related to search parameters or some
> other difference.

Ahem, that could be my bad, I guess I should have explained, I thought it 
was clear from the example command line I supplied.

-nT is the answer you are looking for here.

I used it quickly here to show the missing sub optimals.  My reasoning 
being that if MegaBlast with its large word size and greedy algorithm 
approach could find the suboptimals, the standard version ought to nail 

I tend to use it automatically for near exact DNA/DNA searching, which is 
what this example test was set to do.  So that clears up changes in the 

However, you are _still_ not reporting the sub optimal alignments in your 

This is clear alone from just the sizes of the two files you provided me 
with via your website.  I guess it's just a printing error, you must be 
calculating them.  Probably a simple tweak for you to fix.

node221 /2ndrun/ du -sh ncbi_results.txt
3.4M    ncbi_results.txt

node221 /2ndrun/ du -sh qid1597_results_1.txt
516K    qid1597_results_1.txt

The example gi|27657458|emb|AL844150.6| on that web link I sent before 
shows this.

MegaBlast (jcuff_results_1.txt) finds two such sub alignments, and regular 
blast (jcuff2.blastn,ncbi_results.txt ) finds a whopping 16.

However qid1597_results_1.txt only shows the first alignment from bases 
682 to 1330, with _no_ sub optimals being reported.

Thanks for the update.  We probably ought to kill this thread and take it 
off line if you want to discuss it further.  I doubt it is very 
interesting for folk.



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