]> first line of the .gbk file This should give, for each base or 'ambiguity code' occurring in the sequence, the letter denoting the base, followed by an equals sign, followed by an integer giving the number of times the base occurs in the sequence and its complement. Put a comma between the different bases. E.g. A=50,C=50,G=50,T=50,N=2 Like nucleotide histogram, but giving fraction of times (to 4 decimal places) each nucleotide occurs in the sequence and its complement. In computing these, ignore ambiguity-coded nucleotides. E.g. for the counts given as above one would get A=.2500,C=.2500,G=.2500,T=.2500 Put the matrix of nucleotide counts at each position in known translation start sites here, as a list (pos,nuc)=count,... For example (-10,A)=13,(-10,C)=103,(-10,G)=105,(-10,T)=15,(-9,A)=27, ... where the interpretation is that nucleotide A occurs 13 times at position -10 in known translation start sites, etc. Ignore occurrences of ambiguity-coded nucleotides at each position. Like count matrix, but indicating the fraction of times (to 4 decimal places) each nucleotide occurs at each position, rather than the total counts: e.g. (-10,A)=.0551,(-10,C)=.4364, ... Like frequency matrix, but giving weight. Give values to three decimal places: e.g. (-10,A)=-4.184, ... This should be a list of the form (i,n) where i is an integer and n gives the number of times a score g.t.e. i and l.t. i+1 occurred, for the true start sites. Omit cases i if no score in that range was observed. Also omit all i's corresponding to scores l.t. -50; but include an entry (l.t.-50,n) indicating the number of times a score l.t. -50 occurred. E.g. (l.t.-50,403),(-50,35),(-49,17),... As above, but for all positions in the genome (and its complement). A list of positions in the genome where scores g.t.e. 5.0 occurred but which do NOT correspond to an annotated translation start site. These should be given in the form (p,strand,score) where p indicates position (in top strand, origin 1 co-ordinates), strand = 0 (for top) or 1 (for bottom), and score is given to 3 decimal places. E.g. (15774,0,5.310),(16007,1,7.632),... put comments about your code here ' tag shown below, please split the output up to avoid having the tag in your file before it's end. (i.e. sys.stdout.write("]]") ; sys.stdout.write(">") ]]>