51 lines
1.8 KiB
Factor
51 lines
1.8 KiB
Factor
! Copyright (C) 2020 Bubbler.
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! See http://factorcode.org/license.txt for BSD license.
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USING: assocs help.markup help.syntax strings ;
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IN: rosalind.common
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HELP: fasta>assoc
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{ $values
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{ "str" string }
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{ "assoc" assoc }
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}
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{ $description "Parses a string in FASTA format and returns an assoc of ID - content pairs." } ;
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HELP: amino-table
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{ $values
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{ "value" "A length-64 string of uppercase letters and period" }
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}
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{ $description "A length-64 string that can be used for translation from RNA to amino acid. Each letter denotes an amino acid, and a period indicates a stop codon. The indexing is done by converting UCAG to 0,1,2,3 respectively and interpreting as base 4, highest digit first." } ;
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HELP: protein-mass-table
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{ $values
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{ "value" assoc }
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}
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{ $description "A mapping between the character representation of each amino acid and its monoisotopic mass." } ;
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HELP: rna3>amino
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{ $values
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{ "rna3" "An RNA string of length 3" }
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{ "amino" "A character in amino acid alphabet, or a dot" }
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}
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{ $description "Translates a single codon (a sequence of three RNA nucleotides) into an amino acid. Returns a dot if the input represents a stop codon." } ;
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HELP: rna>protein
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{ $values
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{ "rna" "An RNA string starting with AUG" }
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{ "protein/f" "A protein string, or f" }
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}
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{ $description "Translates an RNA string into a protein string, discarding anything that appears after a stop codon. Returns f if the RNA does not start with the start codon AUG, or a stop codon is not found." } ;
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HELP: reverse-complement
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{ $values
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{ "dna" "A DNA string" }
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{ "dna'" "A DNA string" }
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}
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{ $description "Computes the reverse complement of a DNA string, which represents the opposite strand." } ;
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ARTICLE: "rosalind.common" "rosalind.common"
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{ $vocab-link "rosalind.common" }
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;
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ABOUT: "rosalind.common"
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