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Table 2 Homolmapper reference sequences and scoring schemes

From: Flexible mapping of homology onto structure with Homolmapper

Scoring Algorithm Available Reference Sequences
gaps matched
insertions matched
identity matched, user-chosen, consensus
matrix-based similarity matched, user-chosen, consensus
degen N/A
sloppy matched, user-chosen, consensus
entropy N/A
information content N/A
mutual information N/A
  1. The available reference sequence methods for various homolmapper scoring schemes are shown. Gaps and insertions can be scored by either length or frequency (Figure 1A), but the reference sequence is always the matched sequence. "Degen" and "sloppy" refer to different scoring algorithms using user-defined amino acid sets, as defined in the text. Reference methods are matched (i.e., the sequence matched to the structure), user-chosen (a different sequence in the MSA chosen by the user), and consensus. Some methods are independent of a reference sequence (N/A, not applicable).