seqMatcherAlign             package:SLGI             R Documentation

_F_u_n_c_t_i_o_n_s _t_o _d_o _l_o_c_a_l _a_l_i_g_n_m_e_n_t _o_f _t_w_o _s_e_q_u_e_n_c_e_s _u_s_i_n_g _E_M_B_O_S_S _m_a_t_c_h_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     'seqMatcherAlign' matches two sequences using the EMBOSS matcher
     program. 

     'getAlignStats' extract the statistics from the alignment result
     data.

_U_s_a_g_e:

         seqMatcherAlign(pairNameV,BankIDV,seqBank)
         getAlignStats(alignRes)

_A_r_g_u_m_e_n_t_s:

pairNameV: a vector of gene pair names

 BankIDV: a vector of the sequence IDs in the sequence Bank.

 seqBank: a database of all the sequences 

alignRes: object returned by 'seqMatcherAlign' 

_D_e_t_a_i_l_s:

     'seqMatcherAlign' matches the gene pair names with the sequence
     bank IDs and export the two sequences in to two files: seq1.new
     and seq2.new. Then uses system calls to run EMBOSS matcher program
     to align the two sequences.  The result from matcher is store in
     file "out.matcher".  'seqMatcherAlign' read in this file and
     create a R object summarize the alignment results.

     'getAlignStats' takes the alignment result data and extract the
     statistics of the result in to data.frame.

_V_a_l_u_e:

  names : contains the names of the gene pair

results : contains the alignment statistics: the aligned total length,
          the number of identical match, the number of similar match,
          the number of gaps, and the alignment score

     seq: displays the aligned sequences

_N_o_t_e:

     'pairMatcherAlign' use system calls to run EMBOSS matcher program.
     You must have EMBOSS matcher installed on your computer.

_A_u_t_h_o_r(_s):

     Z. Jiang

_R_e_f_e_r_e_n_c_e_s:

     EMBOSS: The European Molecular Biology Open Software Suite (2000)
     Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6)
     pp276-277

_E_x_a_m_p_l_e_s:

     seq1 <- "RPHEDEKEAIDEAKKMKVPGENEDESKEEEKSQELEEAIDSKEKSTDARDEQGDEGDNEEENNEEDNENENEHTAPPALVMPSPIEMEEQRM"
     seq2 <- "QKYLLKKAIRNFSEYPFYAQNKLIHQQATGLILTEEEKSQELEEKIISKIKKEEHLKKINLKHDYFDLQKKYEKECEILTKLSENLRKEK"
     seq3 <- "IHQQATGLILTKIISKIKKEEHVPGENEDLKKINLKHDYFDLQKKYEKECEILTKLSENLRKEEIENKRKEHELMEQKRREEGIETEKEKSLRHPSSSSSSRRRN"
     seqBank <- list(seq1=list(seq=seq1),seq2=list(seq=seq2),seq3=list(seq=seq3))
     bid <- names(seqBank)
     pnames <- c("seq1","seq3")
     ## Not run: 
     ar <- seqMatcherAlign(pnames, bid, seqBank)
     ar
     getAlignStats(ar)
     ## End(Not run)

