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revision 1.187, Wed Dec 8 21:28:10 2004 UTC revision 1.188, Fri Dec 10 07:04:39 2004 UTC
# Line 3690  Line 3690 
3690  protein collection, and converting it to a set of similarities (one for each of the  protein collection, and converting it to a set of similarities (one for each of the
3691  proteins that are essentially identical to the representative in the nr).  proteins that are essentially identical to the representative in the nr).
3692    
3693    Each entry in @sims is a refence to an array. These are the values in each array position:
3694    
3695    0.   The query peg
3696    1.   The similar peg
3697    2.   The percent id
3698    3.   ?
3699    4.   ?
3700    5.   ?
3701    6.   The start of the match in the query peg
3702    7.   The end of the match in the query peg
3703    8.   The start of the match in the similar peg
3704    9.   The end of the match in the similar peg
3705    10.  E value
3706    11.  ?
3707    12.  Length of query peg
3708    13.  Length of similar peg
3709    14.  Method
3710    
3711  =cut  =cut
3712    
3713  sub sims {  sub sims {

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