Table 1.
The features used by EFIN
| Name | Description | Value and range |
|---|---|---|
| Reference amino acid (AAref) | The reference amino acid of the query position | nominal (A,R,N…V)* |
| Mutant amino acid (AAmut) | The mutant amino acid of the query position | nominal (A,R,N…V)* |
| Frequency of reference amino acid (Fref) | Frequency of reference amino acid at the query position in each block | interval [0,1], with 1 means perfect conservation of reference amino acid |
| Frequency of mutant amino acid (Fmut) | Frequency of mutant amino acid at the query position in each block | interval [0,1], with 1 means that all sequences have the mutant amino acid at the position |
| Shannon Entropy (H) | Shannon entropy in each block at the query position | interval [0,4.322], 0 means no diversity and larger number means more diversity at the position |
| NAS of the first sequence in each block (NASfirst) | Normalized alignment score of the first sequence in each block. | interval [0,1], while 1 means identical sequence to the query human protein |
| Number of sequences in each block (No_all) | Number of total sequences in each block | Interval [0,5000], while 5000 is the cutoff for each MSA |
| Number of sequences which cover the query position in each block (No_qp) | Number of sequences that cover the query position in each block | Interval [0,5000], while 5000 is the cutoff for each MSA |
| No_qp/ No_all (RatioNN) | The ratio of No_qp and No_all | Interval [0,1] |
| Lowest conserved block | The lowest block for which all sequences, together with all the sequences in upper blocks, have the reference amino acid perfectly conserved. | Ordinal (primate block, Non-primate mammal block, non-mammal vertebrate block, invertebrate block, other species block) |
*The 20 amino acids in human proteins.