src/problems/revc.lisp @ 64aa58880d55
EVAL
author |
Steve Losh <steve@stevelosh.com> |
date |
Sat, 23 Feb 2019 12:42:13 -0500 |
parents |
32944636e2d3 |
children |
2735aa6aab79 |
(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)
(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)))