blastlocalhuman.m

function [results]=blastlocalhuman
 
% $LastChangedDate: 2013-01-06 12:45:03 -0600 (Sun, 06 Jan 2013) $
% $LastChangedRevision: 328 $
% $LastChangedBy: jcai $
   
   prompt={'FASTA format:'};
   def={''};
   dlgTitle='Sequence Translation Dialog Box';
   lineNo=10;
   AddOpts.Resize='off';
   AddOpts.WindowStyle='modal';
   AddOpts.Interpreter='none';
   answer=inputdlg(prompt,dlgTitle,lineNo,def,AddOpts);
   
 if ~(isempty(answer)),     
      seq=cellstr(answer{1});
      n=length(seq);
     if (n>=2&length(seq(2))>0)
       if (answer{1}(1)~='>'), error('Sequence is not in FASTA format'); end           
       tempf = tempfilename;
       [fid,Msg] = fopen(tempf,'wt');
       if fid == -1, error(Msg); end
       for (k=1:n),
           fprintf(fid,'%s\n',char(seq(k)));
       end
       fclose(fid);

       olddir=pwd;
       cd('Y:/FAM/HSBlast');
     % Search the sequence against the local blastable database ecoli.nt
     results=blastlocal('inputquery', tempf, 'database', 'HSProteome.fas','program', 'blastp');
     
%     ,'tofile', 'blastlocalhumanres.txt');
 
    %   alndna=readfasta(tempf,2,1);
    %   alnpro=translatealn(alndna);
    %   viewseq(aln2)
    %   viewseqt(alndna.seq)
 %   results = blastreadlocal('blastlocalhumanres.txt',0);
    
    cd(olddir);
    end
 end    

 
 
      res2=blastlocal('inputquery', seq, 'database', 'HSProteome.fas','program', 'blastp','expect',0.001);