85 lines
3.8 KiB
Plaintext
85 lines
3.8 KiB
Plaintext
ribosome update 3 Feb 94
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NAME
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ribosome - translates nucleic acid into protein
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SYNOPSIS
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ribosome [-g gcfile] < input > output
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DESCRIPTION
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ribosome reads a file of one or more nucleic acid sequences
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and writes the corresponding amino acid sequence, in the standard
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one letter code, to output. Ribosome begins translating at the
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first nucleotide in each input sequence and continues to the end.
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If the length of the translated sequence is not divisible by 3,
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ribosome pads the final codon with N's and attempts to use ambi-
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guity rules to translate the final codon. Based on the genetic
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code used, ribosome derives a set of rules to resolve all ambi-
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guities that can possibly be resolved.
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-g read in an alternative genetic code from gcfile. If this
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option is not specified, ribosome uses the universal
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genetic code.
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gcfile - This file specifies an alternative genetic code. An
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example is shown below. ribosome reads the first 64 legal
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capital letters as amino acids. Consequently, lowercase letters
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can be used for annotation purposes, as shown in the example.
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All non-amino acid characters are ignored.
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sgc2 - yeast mitochondrial genetic code
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second position
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first position ------------------------------- third position
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(5' end) u c a g (3' end)
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-----------------------------------------------------------------
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u F S Y C u
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F S Y C c
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L S * W a
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L S * W g
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-----------------------------------------------------------------
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c T P H R u
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T P H R c
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T P Q R a
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T P Q R g
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-----------------------------------------------------------------
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a I T N S u
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I T N S c
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M T K R a
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M T K R g
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-----------------------------------------------------------------
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g V A D G u
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V A D G c
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V A E G a
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V A E G g
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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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; one or more comment lines (optional)
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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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SEE ALSO
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getob
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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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REFERENCE
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Fristensky, B. (1993) Feature expressions: creating and manipulating
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sequence datasets. Nucleic Acids Research 21:5997-6003.
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