On half gapped seed.

In this paper, we proposed a new type of seed for Blast-like homology search tools called "half seed''. This new seed is better than the "consecutive seed'' used by the original Blast tools in both sensitivity and efficiency. When compared with the "gapped seed'', which is proposed together with a new Blast-like searching tool, PatternHunter, this new seed offers a much wider range of choices for performing tradeoff between sensitivity and efficiency. This property is especially useful when some searching applications want to get more precise results with limitation on hardware resources, or vice versa.