Linear predictive coding representation of correlated mutation for protein sequence alignment

BMC Bioinformatics

Table 1 Selected parameters for the different combination of scoring terms.

w_mut, w_sec, w_cor, and d₀ denote the corresponding notations in alignment score function, and g_open, g_ext, and base denote gap-open cost, gap-extension cost, and baseline parameter used for dynamic programming procedure. PPA and PPA_SS denote profile-profile alignment without and with secondary structure prediction, respectively, CMPA denote alignment solely using CM profile, and CMPA_PPA and CMPA_PPA_SS denote alignment combining CM profile with PPA and PPA_SS, respectively.

ISSN: 1471-2105