Greetings I ran a test on the the 2.2.13 BLAST that I thought the list might find interesting. (Thanks to Joe Landman for putting it on the list, I thought I was on that particular NCBI distribution but never saw the message until Joe put it here.) I made a database out of the TIGR gene index for pig, SSGI.021105 I made a test query out of 200 70mers based on 5 sequences from SSGI.021105. I ran on a simple test on a Solaris/Sparc64 using time blastall [-V F] -p blastn -i test.fa -d SSGI.021105 > test.blast yielding 2.2.12 2.2.13 no -V 2.2.13 with -V F user 1m 39.8s 1m 50.3s 0m 9.2s real 1m 46.9s 1m 57.7 0m 9.5s sys 0m 6.3s 0m 6.3s 0m 0.3s A diff on the output between v.12 and v.13(no V -F) produces only differences in the header because the version numbers are different. The diff between v.13(no V -F) and v.13 produces small differences in the scores and e-values. For example: < NP1115201 GB|AY277629.1|AAQ24490.1 type XVII collagen [Sus scrofa] 139 4e-33 < AJ656543 34 0.18 < BP160342 32 0.73 < TC237977 32 0.73 < TC212301 32 0.73 < CJ009554 30 2.9 < AJ657806 30 2.9 < BI344938 30 2.9 < AJ651764 30 2.9 < TC220684 UP|S3A3_HUMAN (Q12874) Splicing factor 3A subunit 3 (Sp... 30 2.9 --- > NP1115201 GB|AY277629.1|AAQ24490.1 type XVII collagen [Sus scrofa] 138 6e-33 > AJ656543 34 0.19 > BP160342 32 0.75 > TC237977 32 0.75 > TC212301 32 0.75 > CJ009554 30 3.0 > AJ657806 30 3.0 > BI344938 30 3.0 > AJ651764 30 3.0 > TC220684 UP|S3A3_HUMAN (Q12874) Splicing factor 3A subunit 3 (Sp... 30 3.0 So, it looks to be significantly faster. Cheers Mike