HHMER3, a software suite for protein sequence analysis, is highlighted here as the first profile-based method running at close to BLAST's speed. Significant and innovative computational advances are presented that allow notoriously slow but accurate profile searches to approach BLAST in speed, while retaining and even gaining accuracy. Test this new method out! It can also run on a large sequence database -- not only on databases of alignments -- and it has iterative capabilities similar to PSI-BLAST.