AllOrfs                package:GeneR                R Documentation

_G_e_t _O_R_F_s _f_r_o_m _a _s_e_q_u_e_n_c_e

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

     Get ORFs (Open Reading Frame) from a sequence. Codon start is atg,
     stop is taa,tga,tag.

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

     allOrfs(phase = NULL,seqno=0,start="atg",
                        stop=c("taa","tag","tga"))
     maxOrf(seqno=0,phase = NULL,start="atg",
                        stop=c("taa","tag","tga"))

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

   seqno: Integer. Sequence number (bufseq)

   phase: Integer. 1,2 or 3, NULL for all phases

   start: "start" sequences

    stop: "stop" sequences

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

     allOrf return a table. NULL if no Orfs.

     maxOrf return size of largest Orf, -1 if no Orf.

     All functions return NA if error.

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

     A. Lucas and Vincent Lefort

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

     s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
     placeString(s)

     allOrfs(phase = NULL,seqno=0)
     maxOrf()

     # On complemetary strand:
     sc <- getSeq(0,1)
     placeString(sc,seqno=1)
     allOrfs(phase = NULL,seqno=1)

     # All orfs :
     rbind(allOrfs(seqno=0),allOrfs(seqno=1))

