# -*- Mode: Darwin -*- # CodonTools -- Tools for manipulating Codons # Author : Gina CANNAROZZI # Created On : 2 Aug 2001 # Summary of What is Available for conversions # #AToInt convert a 1 letter amino acid code to an integer #AAAToInt convert a 3 letter amino acid code to an integer #AminoToInt convert a amino acid name to an integer #BToInt (old NToInt) convert a 1 letter nucleic acid code to an integer #BBBToInt (old NucToInt) convert a 3 letter nucleic acid code to an integer #BaseToInt (old NucleicToInt) convert nucleic acid name to an integer #IntToA, IntToAAA, IntToAmino, IntToB (IntToN), IntToBBB(IntToNuc), #IntToBase (IntToNucleic) #CodonToA (GenCode) convert a codon into the corresponding amino acid 1 letter code #CodonToInt (GenCodeToInt) convert a codon into the corresponding amino acid integer # #CodonToCInt (NucToCode) a'convert a 3-letter codon into a integer from 0 to 64 #CIntToCodon (CodeToNuc) convert an integer from 1 to 64 into 3-letter codon # #AToCodon (AToGenCode)- convert a 1 letter amino acid code to a list of codons [codon 1, codon 2, ... ] #IntToCodn (IntToGenCode)- convert a 1 letter amino acid code to a list of codons [codon int 1, codon int 2, ... ] # #CIntToInt (CodonToInt)- convert a number from 1 to 64 to the corresponding amino acid integer #CIntToA (CodonToA)- convert a number from 1 to 64 to the corresponding amino acid 1 letter code #CIntToAAA (CodonToAAA)- convert a number from 1 to 64 to the corresponding amino acid 3 letter code #CIntToAmino (CodonToAmino)- convert a number from 1 to 64 to the corresponding amino acid name #AToCInt amino acid 1 letter code to codon integer #IntToCInt amino acid integer to codon integer # # AToCInt: convert 1 letter amino acid to a codon integer from 1..64 # AToCInt_array := [ [37, 38, 39, 40], [9, 11, 25, 26, 27, 28], [2, 4], [34, 36], [58, 60], [17, 19], [33, 35], [41, 42, 43, 44], [18, 20], [13, 14, 16], [29, 30, 31, 32, 61, 63], [1, 3], [15], [62, 64], [21, 22, 23, 24], [10, 12, 53, 54, 55, 56], [5, 6, 7, 8], [59], [50, 52], [45, 46, 47, 48] ]: AToCInt := proc(AA:string) #AToInt returns 0 to 21- 0 for error, 21 for X if AA = '$' then return([49,51,57]) fi: aa := AToInt(uppercase(AA)): if aa = 0 or aa > 21 then error('not a valid amino acid abbreviation') elif aa = 21 then return([]) else AToCInt_array[aa] fi: end: # # IntToCInt: convert amino acid integer to a codon integer from 1..64 # IntToCInt := proc(AA:{posint,'$'}) #AToInt returns 0 to 21- 0 for error, 21 for X if AA = '$' or AA = 22 then return([49,51,57]) fi: if AA = 0 or AA > 22 then error('not a valid amino acid ') elif AA = 21 then return([]) else AToCInt_array[AA] fi: end: AToCodon_array := [ ['GCA', 'GCC', 'GCG', 'GCT'], ['AGA', 'AGG', 'CGA', 'CGC', 'CGG', 'CGT'], ['AAC', 'AAT'], ['GAC', 'GAT'], ['TGC', 'TGT'], ['CAA', 'CAG'], ['GAA', 'GAG'], ['GGA', 'GGC', 'GGG', 'GGT'], ['CAC', 'CAT'], ['ATA', 'ATC', 'ATT'], ['CTA', 'CTC', 'CTG', 'CTT', 'TTA', 'TTG'], ['AAA', 'AAG'], ['ATG'], ['TTC', 'TTT'], ['CCA', 'CCC', 'CCG', 'CCT'], ['AGC', 'AGT', 'TCA', 'TCC', 'TCG', 'TCT'], ['ACA', 'ACC', 'ACG', 'ACT'], ['TGG'], ['TAC', 'TAT'], ['GTA', 'GTC', 'GTG', 'GTT'] ]: # # AToCodon: convert 1 letter amino acid to 3 letter codon list # AToCodon := proc(AA:string) if AA = '$' then return([TAA,TAG,TGA]) fi: aa := AToInt(uppercase(AA)): if aa = 0 then error('not a valid amino acid code') elif aa = 21 then return([]) else AToCodon_array[aa] fi: end: # # IntToCodon: convert amino acid integer to 3 letter codon list # IntToCodon := proc(AA:integer) if AA <= 0 or AA > 22 or AA=21 then error('not a valid amino acid code') elif AA = 22 then return([TAA,TAG,TGA]) else AToCodon_array[AA] fi: end: MakeOrderedCodonList := proc() printf('codon_list := ['): for b1 in [A,C,G,T] do for b2 in [A,C,G,T] do for b3 in [A,C,G,T] do printf('''%s'',',b1.b2.b3): od: od: od: printf('];'): end: # # CodonToCInt (NucToCode): convert codon to codon position # CodonToCInt_list := [-100,0,1,2,3,3,-100]; NucToCode := proc( bbb:string ) if length(bbb) < 3 then 0 else max( 0, 16 * CodonToCInt_list[BToInt(bbb[1])+1] + 4 * CodonToCInt_list[BToInt(bbb[2])+1] + CodonToCInt_list[BToInt(bbb[3])+1] + 1 ) fi end: CodonToCInt := eval(NucToCode): # # CIntToCodon (CodeToNuc): convert codon position to codon # CodeToNuc := proc (pos: posint) if pos > 64 then error ('Invalid codon position') fi; p1 := pos - 1; p3 := mod(p1, 4); p1 := (p1 - p3) / 4; p2 := mod(p1, 4); p1 := (p1 - p2) / 4; IntToB(p1+1).IntToB(p2+1).IntToB(p3+1) end: CIntToCodon := eval(CodeToNuc): # # CIntToInt (CodonToInt): convert codon position to amino acid integer # # the old name was not retained as it is the new name for something else CIntToInt_array := [ 12, 3, 12, 3, 17, 17, 17, 17, 2, 16, 2, 16, 10, 10, 13, 10, 6, 9, 6, 9, 15, 15, 15, 15, 2, 2, 2, 2, 11, 11, 11, 11, 7, 4, 7, 4, 1, 1, 1, 1, 8, 8, 8, 8, 20, 20, 20, 20, 22, 19, 22, 19, 16, 16, 16, 16, 22, 5, 18, 5, 11, 14, 11, 14 ]: CIntToInt := proc(cod:posint) if cod <= 64 then CIntToInt_array[cod] else error('codon Int too high') fi end: # # CIntToA (CodonToA): convert codon position to one amino acid letter # # the old name was not retained as it is the new name for something else CIntToA := proc (codon:posint) if codon > 64 then error('invalid codon integer value') fi: IntToA(CIntToInt_array[codon]) end: # # CIntToAAA (CodonToAAA): convert codon position to three letter amino acid name # CodonToAAA := proc(codon:posint) if codon > 64 then error('invalid codon integer value') fi: IntToAAA(CIntToInt_array[codon]) end: CIntToAAA := eval(CodonToAAA): # # CIntToAmino (CodonToAmino): convert codon position to amino acid name # CIntToAmino := proc(codon:posint) if codon > 64 then error('invalid codon integer value') fi: IntToAmino(CIntToInt_array[codon]) end: CodonToAmino := eval(CIntToAmino): # Alternative genetic codes taken from # http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c#SG11 # and edited to preserve the AAs and Start lines # (in this format it is easier to maintain and more efficient to load) # Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG # Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG # Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG TranslationCodeSource := [ ['1. The Standard Code (transl_table=1)', 'FFLLSSSSYY$$CC$WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG', '---M---------------M---------------M----------------------------'], ['2. The Vertebrate Mitochondrial Code (transl_table=2)', 'FFLLSSSSYY$$CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS$$VVVVAAAADDEEGGGG', '--------------------------------MMMM---------------M------------'], ['3. The Yeast Mitochondrial Code (transl_table=3)', 'FFLLSSSSYY$$CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG', '----------------------------------MM----------------------------'], ['4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code (transl_table=4)', 'FFLLSSSSYY$$CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG', '--MM---------------M------------MMMM---------------M------------'], ['5. The Invertebrate Mitochondrial Code (transl_table=5)', 'FFLLSSSSYY$$CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG', '---M----------------------------MMMM---------------M------------'], ['6. The Ciliate, Dasycladacean and Hexamita Nuclear Code (transl_table=6)', 'FFLLSSSSYYQQCC$WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG', '-----------------------------------M----------------------------'], ['7. Table has been deleted (transl_table=7)','',''], ['8. Table has been deleted (transl_table=8)','',''], ['9. The Echinoderm and Flatworm Mitochondrial Code (transl_table=9)', 'FFLLSSSSYY$$CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG', '-----------------------------------M---------------M------------'], ['10. The Euplotid Nuclear Code (transl_table=10)', 'FFLLSSSSYY$$CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG', '-----------------------------------M----------------------------'], ['11. The Bacterial and Plant Plastid Code (transl_table=11)', 'FFLLSSSSYY$$CC$WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG', '---M---------------M------------MMMM---------------M------------'], ['12. The Alternative Yeast Nuclear Code (transl_table=12)', 'FFLLSSSSYY$$CC$WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG', '-------------------M---------------M----------------------------'], ['13. The Ascidian Mitochondrial Code (transl_table=13)', 'FFLLSSSSYY$$CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG', '-----------------------------------M----------------------------'], ['14. The Alternative Flatworm Mitochondrial Code (transl_table=14)', 'FFLLSSSSYYY$CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG', '-----------------------------------M----------------------------'], ['15. Blepharisma Nuclear Code (transl_table=15)', 'FFLLSSSSYY$QCC$WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG', '-----------------------------------M----------------------------'], ['16. Chlorophycean Mitochondrial Code (transl_table=16)', 'FFLLSSSSYY$LCC$WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG', '-----------------------------------M----------------------------'], ['17. Table does not exist (transl_table=17)','',''], ['18. Table does not exist (transl_table=18)','',''], ['19. Table does not exist (transl_table=19)','',''], ['20. Table does not exist (transl_table=20)','',''], ['21. Trematode Mitochondrial Code (transl_table=21)', 'FFLLSSSSYY$$CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG', '-----------------------------------M---------------M------------'], ['22. Scenedesmus obliquus mitochondrial Code (transl_table=22)', 'FFLLSS$SYY$LCC$WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG', '-----------------------------------M----------------------------'], ['23. Thraustochytrium Mitochondrial Code (transl_table=23)', 'FF$LSSSSYY$$CC$WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG', '--------------------------------M--M---------------M------------']]: AltGenCode := proc( gencode:posint, codon:string, pos:posint ) global AltGenCode_array; if not assigned(AltGenCode_array) then n := length(TranslationCodeSource); AltGenCode_array := CreateArray(1..n,1..64): for i to n do # ['T','C','A','G'] is [4,2,1,3] in integers Ti := TranslationCodeSource[i]; if Ti[2]='' then next fi; j := 1; for B1 in [4,2,1,3] do for B2 in [4,2,1,3] do for B3 in [4,2,1,3] do k := 16*B1 + 4*B2 + B3 - 20; if Ti[3,j]='-' then AltGenCode_array[i,k] := [Ti[2,j]] else AltGenCode_array[i,k] := [Ti[2,j],Ti[3,j]] fi; j := j+1 od od od; od; fi; if length(codon) <> 3 then error(codon,'codon must be of length three') elif gencode > length(AltGenCode_array) then error(args,'invalid alternative genetic code') fi; index := CodonToCInt(uppercase(codon)); if index=0 then ['X'] # it contains an invalid base or X elif nargs=3 then if pos>1 then AltGenCode_array[gencode,index,1..1] else AltGenCode_array[gencode,index,2..-1] fi else AltGenCode_array[gencode,index] fi end: Ascii_symbols := ['NULL','SOH','STX','ETX','EOT','ENQ','ACK','BEL','BS','HT','LF', 'VT','FF','CR','SO','SI','DLE','DC1','DC2','DC3','DC4', 'NAK','SYN','ETB','CAN','EM','SUB','ESC','FS','GS','RS', 'US','SP','!','"','#','$','%','&','''','(', ')','*','+',',','-','.','/','0','1','2', '3','4','5','6','7','8','9',':',';','<', '=','>','?','@','A','B','C','D','E','F', 'G','H','I','J','K','L','M','N','O','P', 'Q','R','S','T','U','V','W','X','Y','Z', '[','\\',']','^','_','`','a','b','c','d', 'e','f','g','h','i','j','k','l','m','n', 'o','p','q','r','s','t','u','v','w','x', 'y','z','{','|','}','~','DEL']; # IntToAscii is now in the kernel # AsciiToInt is now in the kernel # Nici's system for using one character codes for codons # #T = 0, C = 1, A = 2, G = 3 # #ascii code = 16*(codon 1) + 4*(codon 2) + (codon 3) + 48 # #i.e. # #TTT = 48 (ascii '0') #TTC = 49 (ascii '1') #... #GGA = 110 (ascii 'n') #GGG = 111 (ascii 'o') # #I then use (ascii code - 48) as an index into the string #"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG" GenCodeToCodonSymbol := proc (cs:string) if length(cs) <> 3 then error('length of codon must be 3 characters') fi; val := [0,0,0]; for i to 3 do val[i] := SearchArray(cs[i],[T,C,A,G]) -1; od; asciicode := 16*(val[1]) + 4*(val[2]) + (val[3]) + 48; IntToAscii(asciicode); end: CodonSymbolToGenCode := proc(str:string) if str < '/' or str > 'I' then error('invalid input'); fi; ret := ''; index := [T,C,A,G]; for i to length(str) do num := AsciiToInt(str)-48; rem := num-iquo(num,16)*16; one := index[iquo(num,16)+1]; two := index[iquo(rem,4)+1]; rem := rem-iquo(rem,4)*4; three := index[rem+1]; ret := ret.one.two.three od; end: CodonSymbolToA := proc(cs:string) index := 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG'; aastring := CreateString(length(cs)); for i to length(cs) do aastring[i] := IntToA(CodonToInt(CodonSymbolToGenCode(cs[i]))); od; aastring; end: