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)

