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BLAST maximal segment pair with Karlin-Altschul E-value

Source: R/blastp_native.R
morie_blastp.Rd

MSP = highest-scoring ungapped local segment pair (Altschul et al. 1990 Sec. 2a); E = K m n exp(-lambda S) (Karlin-Altschul extreme-value statistics); p = 1 - exp(-E).

Usage

morie_blastp(
  query,
  subject,
  match = 1,
  mismatch = -1,
  K = 0.1,
  lam = 1,
  score_matrix = NULL
)

Arguments

query, subject

Sequences (character strings).

match, mismatch

Substitution scores.

K, lam

Karlin-Altschul parameters.

score_matrix

Optional named list keyed "a|b".

Value

A list with elements score, e_value, p_value, q_start, s_start, length, method.

References

Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410.

Examples

V <- c(1, 2, 3, 4, 5, 6, 7, 8)
morie_blastp(V, V)
#> $score
#> [1] 1
#> 
#> $e_value
#> [1] 0.03678794
#> 
#> $p_value
#> [1] 0.03611949
#> 
#> $q_start
#> [1] 0
#> 
#> $s_start
#> [1] 0
#> 
#> $length
#> [1] 1
#> 
#> $method
#> [1] "BLAST MSP + Karlin-Altschul E-value (Altschul 1990)"
#>