Those two sites use BLAST with different default parameters : Match/Mismatch Scores, gap costs, etc. Set the same values and compare, they should give you more similar result.

If you need searching homologous groups, use NCBI or EMBL etc. are no problems, If you need exact identification with type species, I suggest extaxon-e database (http://eztaxon-e.ezbiocloud.net/). In case of public DBs many sequences are uploaded mis-identified or un-identified (just described as environmental sample) state.

Dr Kwon is rightm you cannot rule out the fact of wrong identifications in Genebank. Be careful and trust BLAST only when you have several homologsfor your sequence from the same species.

Thanks Alex ignatov and Kaekyoung kwon for your reply. I have one question for alex regarding ezbiocloud.net i.e. in this website i am getting two options- EzGenome and EzTaxon. so which one to prefer?

In your case, choose EzTaxon and one's more identify. of course you should make an id and pw for use identify menu.

Ali, I agree to Dr. Kwon. Good luck to you!

Hi,

I think NCBI is accurate. But before BLAST search you should run your sequence on clustalW software then you will get better matching. Good luck.

When you use EzTaxon do note that many times identification could be somewhat tricky, as similar identity could be obtain for more then one species, and many times a change in few nucleotides will switch you to another species altogether... I did not find a good solution yet but the environmental microbiologists around here tend to simply pick the first species name on the list.

Best of luck.

Yoram