prot2nuc update 10 Aug 94 NAME prot2nuc - reverse translates protein into nucleic acid SYNOPSIS prot2nuc [-ln -gn] < input > output DESCRIPTION prot2nuc reads a file containing an amino acid sequence and writes the corresponding reverse translated nucleic acid sequence, using the standard IUPAC-IUB ambiguity codes to output. The amino acid sequence may contain internal stop '*' characters. That is, all legal amino acid characters will be processed. -ln print n amino acids/codons per line. (default = 25) -gn number the amino acid sequence every n amino acids/codons. (defalut = 5) If l is not evenly divisible by g, the defaults are used. input - If the first line of the file begins with '>' or ';', input will be read as the standard .wrp (Pearson) format, such as that produced by getob: >name sequence lines Otherwise, it will be assumed that the file ONLY contains sequence, and all legal IUPAC/IUB DNA characters will be read as sequence. output - The output begins with a header, listing the both 1 and 3 letter amino acid codes [J. Biol. Chem. 243, 3557-3559 (1968)], as well as the nucleic acid ambiguity codes [Cornish- Bowden (1985) Nucl. Acids Res. 13:3021-3030.]. The amino acid sequence, along with its reverse translation, are then printed on lines of l amino acids/codons, numbering every g amino acids/codons. Non-ambiguous nucleotides appear capitalized, while ambiguous nucleotides are in lowercase. A sample output file appears below: PROT2NUC Version 8/10/94 IUPAC-IUP AMINO ACID SYMBOLS [J. Biol. Chem. 243, 3557-3559 (1968)] Phe F Leu L Ile I Met M Val V Ser S Pro P Thr T Ala A Tyr Y His H Gln Q Asn N Lys K Asp D Glu E Cys C Trp W Arg R Gly G STOP * Asx B Glx Z UNKNOWN X IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE [Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030.] Symbol Meaning | Symbol Meaning ------------------------------------+--------------------------------- G Guanine | k G or T A Adenine | s G or C C Cytosine | w A or T T Thymine | h A or C or T U Uracil | b G or T or C r Purine (A or G) | v G or C or A y Pyrimidine (C or T) | d G or T or A m A or C | n G or A or T or C pI39 5 10 15 20 M E K K S L A A L S F L L L L V L F V A ATGGArAArAArTCnCTnGCnGCnCTnTCnTTyCTnCTnCTnCTnGTnCTnTTyGTnGCn AGyTTr TTrAGy TTrTTrTTrTTr TTr 25 30 35 40 Q E I V V T E A N T C E H L A D T Y R G CArGArAThGTnGTnACnGArGCnAAyACnTGyGArCAyCTnGCnGAyACnTAyCGnGGn TTr AGr 45 50 55 60 V C F T N A S C D D H C K N K A H L I S GTnTGyTTyACnAAyGCnTCnTGyGAyGAyCAyTGyAArAAyAArGCnCAyCTnAThTCn AGy TTr AGy 65 70 G T C H D W K C F C T Q N C GGnACnTGyCAyGAyTGGAArTGyTTyTGyACnCArAAyTGy With the Universal Genetic code, ambiguity symbols make it possible to represent all possible codons for an amino acid using two output lines. It is important to realize that the ambiguities on each line can not be combined. For example, CTn and TTr represent all codons for Leucine. However, attempting to combine them into a single triplet, yTn, would be incorrect. For example, TTT and TTC are codons for Phenylalanine, not Leucine. FUTURE PLANS 1. It wouldn't be hard to have the output printed as nucleic acid sequences in Perason format, so that the output could be read back into GDE. I don't know why you would want to do this, but it could be done. 2. Right now, only the Universal Genetic Code is used, but it should be possible to read in alternative genetic codes, have prot2nuc figure out the ambiguity rules (as is already done in ribosome) and print out the appropriate ambiguous codons. 3. It might be useful to have each possible codon printed out, rather than ambiguous codons. This would take up a lot more space and wouldn't be as pretty. If there's a lot of demand I could do this. AUTHOR Dr. Brian Fristensky Dept. of Plant Science University of Manitoba Winnipeg, MB Canada R3T 2N2 Phone: 204-474-6085 FAX: 204-261-5732 frist@cc.umanitoba.ca