Table 2 Sequence comparison methods and parameters
From: Testing statistical significance scores of sequence comparison methods with structure similarity
Method | Abbreviation | Version | Matrix | Gap open penalty | Gap extension penalty | Number of randomizations |
|---|---|---|---|---|---|---|
Paracel SW e-value | pc e | - | BLOSUM62 | 3*IS * | 0.3*IS * | 0 |
Biofacet SW Z-score | bf z | 2.9.6 | BLOSUM62 | 12 | 1 | 100 |
NCBI BLAST e-value | bl e | 2.2.9 | BLOSUM62 | 12 | 1 | 0 |
FASTA e-value | fa e | 3.4t24 | BLOSUM62 | 12 | 1 | 0 |
SSEARCH e-value | ss e | 3.4t24 | BLOSUM62 | 12 | 1 | 0 |
ParAlign SW e-value | pa e | 4.0.0 | BLOSUM62 | 12 | 1 | 0 |