BLAST service at TAIR

Sue Rhee rhee at acoma.Stanford.EDU
Thu Feb 17 17:47:52 EST 2000

Dear Arabidopsis researchers,

We are trying to ameliorate the problem of performance with the TAIR BLAST
service. We are currently implementing and testing an additional BLAST
server (using WU BLAST) and also trying to configure the current BLAST
server to separate short and long input sequence queries. In order to
improve the performance in the short term, we would like to impose the
following limits on the input sequence size:

BLASTN = 25000 bp (All datasets)
BLASTX = 25000 bp (All datasets)
BLASTP = 5000 aa  (All datasets)
TBLASTN = 1000 aa (Large datasets. ArabidopsisN, etc)
TBLASTN = 5000 aa (Small datasets, New GenBank and similar size datasets)
TBLASTX = 1000 bp (Large datasets. ArabidopsisN, etc)
TBLASTX = 5000 bp (Small datasets, New GenBank and similar size datasets)

This could be summarized as:

nucleotide queries  - 25 kb except tblastx/large datasets (1 kb) and
tblastx/small datasets (5 kb)

amino acid queries - 5000 aa except tblastn/large datasets (1000 aa)

Large datasets = GenBankPlus, GenBankMinus, Protein, GenBank >10K, All

Please let us know if you have any problems with these limits.

The TAIR Team
curator at


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