Sensitivity Analysis of Boosting PSI-Blast with Case Study on Subcellular Localization

This paper studies the sensitivity of PSI-BLAST with respect to the ´h´ parameter. Observing that the standard PSI-BLAST is sensitive to parameter ´h´ in the high-value region, we propose a new technique, called boosting PSI- BLAST, to reduce the sensitivity. By constraining ´h´ to a small value first so as to reduce the chance of early corruption and then relaxing it gradually to increase divergence, the boosting PSI-BLAST not only can reduce the sensitivity to h-value, but also may strike a good balance between corruption and divergence in profiles. Tests on Reinhardt and Hubbard´s eukaryotic protein dataset verify that our method is better in reducing the sensitivity of profile alignment scores to h-value than the standard PSI-BLAST.