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