src/problems/revc.lisp @ b3598dc7ef5c

(in-package :rosalind)

;; DNA is made up of two strands running in opposite directions, usually twisted
;; into a double helix, with the bases bonded:
;;
;;    …sP-+-sP-+-sP-+-sP-+-sP…
;;        |    |    |    |
;;        C    A    T    G          s = sugar molecule
;;       G    T    A    C           p = phosphate anion
;;       |    |    |    |
;;   …sP-+-sP-+-sP-+-sP-+-sP…
;;
;; Each base will only bond with one specific other base:
;;
;; * Adenine/Thymine
;; * Cytosine/Guanine
;;
;; The "complement" of a base is the other base it will bond to.
;;
;; Two bonded bases are called a base pair (bp).  Generally DNA lengths are
;; specified in numbers of base pairs.
;;
;; If we know the order of the bases in one strand, we can figure out the other
;; strand by taking the reverse complement.
;;
;; The problem summaries don't really make it clear what "running in opposite
;; directions" means.  I think I remember there being something about DNA having
;; polarized ends, with one end being called 3′ and the other being 5′, but I'm
;; not 100% sure.

(defun nreverse-complement (dna)
  (flet ((dna-complement (base)
           (case base
             (#\A #\T)
             (#\T #\A)
             (#\G #\C)
             (#\C #\G))))
    (map-into dna #'dna-complement dna)
    (nreverse dna)))

(defun reverse-complement (dna)
  (nreverse-complement (copy-seq dna)))

(define-problem revc (data string)
    "AAAACCCGGT"
    "ACCGGGTTTT"
  "Return the reverse complement of `data`."
  (nreverse-complement (delete #\newline data)))