translate               package:seqinr               R Documentation

_T_r_a_n_s_l_a_t_e _n_u_c_l_e_i_c _a_c_i_d _s_e_q_u_e_n_c_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function translates nucleic acid sequences to the
     corresponding peptide sequence. It can translate in any of the 3
     forward or three reverse sense frames. In the case of reverse
     sense, the reverse-complement of the sequence is taken. It can
     translate using the standard (Universal) genetic code and also
     with a selection of non-standard codes.

_U_s_a_g_e:

     translate(seq, frame = 0, sens = "F", numcode = 1)

_A_r_g_u_m_e_n_t_s:

     seq: an object of class 'seq'. 

   frame: Frame(s) (0,1,2) to translate. By default the frame '0' is
          used. 

    sens: Sense to translate: 'F' for forward sense and 'R' for revers
          sense. 

 numcode: The number of the code to use. By default the standard
          genetic code is used. 

_D_e_t_a_i_l_s:

     The following genetic codes are described here. The number
     preceding each code corresponds to 'numcode'. 

   _1 standard 

   _2 vertebrate.mitochondrial 

   _3 yeast.mitochondrial 

   _4 protozoan.mitochondrial+mycoplasma 

   _5 invertebrate.mitochondrial 

   _6 ciliate+dasycladaceal 

   _9 echinoderm+flatworm.mitochondrial 

   _1_0 euplotid 

   _1_1 bacterial+plantplastid 

   _1_2 alternativeyeast 

   _1_3 ascidian.mitochondrial  

   _1_4 alternativeflatworm.mitochondrial 

   _1_5 blepharism 

   _1_6 chlorophycean.mitochondrial 

   _2_1 trematode.mitochondrial 

   _2_2 scenedesmus.mitochondrial 

   _2_3 hraustochytrium.mitochondria 

_V_a_l_u_e:

     'translate' returns a vector of character containing the peptide
     sequence in the standard one-letter IUPAC code. Termination (STOP)
     codons are translated as the character '*'.

_A_u_t_h_o_r(_s):

     D. Charif

_R_e_f_e_r_e_n_c_e_s:

     The genetic codes have been taken from the ncbi taxonomy database:
     <URL: 
     http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c >.
     Last update October 05, 2000.
      The IUPAC one-letter code for aminoacids is described at:  <URL:
     http://www.chem.qmul.ac.uk/iupac/AminoAcid/>

     'citation("seqinr")'

_S_e_e _A_l_s_o:

     'SEQINR.UTIL'

_E_x_a_m_p_l_e_s:

     a=read.fasta(File=system.file("sequences/malM.fasta",package ="seqinr"))
     translate(a[[1]])
     translate(a[[1]],3,"R",6)

