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 it. 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 ordering. However, you are _still_ not reporting the sub optimal alignments in your report. 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. Best, J.