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1 : overbeek 1.1 <h1>An Explanation of the SEED Evidence Codes</h1>
2 :    
3 :     Within the SEED, we use evidence codes to reflect significant factors
4 :     that go into making assignments of function. Some of these codes are
5 :     computed and reflect information that we consider particularly
6 :     useful. Others are used to reflect experimental evidence of function.
7 :    
8 :     <h2>icw(n): in cluster with</h2>
9 :    
10 :     This code indicates that the PEG occurs in a cluster with <i>n</i>
11 : overbeek 1.2 other genes from the same subsystem (very strong evidence). There may
12 :     be several of these for a PEG (up to one for each subsystem the PEG
13 :     occurs in).
14 : overbeek 1.1
15 :     <h2>isu: in subsystem unique -- the only entry in a subsystem cell</h2>
16 :    
17 :     This code indicates that the PEG occurs in a subsystem, and it is the
18 :     only PEG for that genome that has been assigned the functional role
19 :     (i.e., the cell in the spreadsheet contains a single entry). This
20 :     means that, if you wish to change an annotation, you should discuss it
21 :     with the owner of the subsystem.
22 :    
23 : overbeek 1.3 <h2>idu(n): in subsystem duplicates</h2>
24 : overbeek 1.1
25 :     This code indicates that the PEG occurs in a subsystem, but it is
26 :     in a cell of the spreadsheet containing duplicates (and it is not
27 :     clustered with other genes connected to the same subsystem).
28 :     In this case, you may make a change without notifying the owner of the
29 :     subsystem, since you are probably disambuating the situation to his
30 :     benefit.
31 : overbeek 1.3
32 : overbeek 1.5 <h2>ff: in FIGfam</h2>
33 : overbeek 1.3
34 : overbeek 1.5 This code indicates that the protein-encoding gene is included in a FIGfam.
35 : overbeek 1.3
36 : overbeek 1.5 <h2>cwn: Clustered with Nonhypothetical</h2>
37 : overbeek 1.3
38 : overbeek 1.5 This code indicates that the protein-encoding gene is functionally
39 :     coupled to at least one other protein that has been assigned a
40 :     function that is considered "nonhypothetical". The functional
41 :     coupling score must be 5 or more for this code to apply. This means
42 :     that the gene co-occurs on the chromosome in at least 5 instances of
43 :     genomes that are not close strains with another gene that is
44 :     considered nonhypothetical.
45 :    
46 :     <h2>cwn: Clustered with Hypothetical</h2>
47 :    
48 :     This code indicates that the protein-encoding gene is functionally
49 :     coupled to at least one other protein that has been assigned a
50 :     function, but none that is considered "nonhypothetical". The functional
51 :     coupling score must be 5 or more for this code to apply. This means
52 :     that the gene co-occurs on the chromosome in at least 5 instances of
53 :     genomes that are not close strains with at least one other gene, but none that is
54 :     considered nonhypothetical.
55 :    
56 :     <h2> dlit: Direct Literature References to the Gene Exist </h2>
57 :    
58 :     This code is used to indicate that at least one paper (that is a
59 :     "nongenome paper" in the sense that it does not reference hundreds of
60 :     genes) is associated with this gene.
61 :    
62 :     <h2> ilit: Indirect Literature References to the Gene Exist </h2>
63 :    
64 :     This code is used to indicate that at least one paper (that is a
65 :     "nongenome paper" in the sense that it does not reference hundreds of
66 :     genes) is associated with a gene assigned the same functional role,
67 :     but none to this gene itself (as far as we know).
68 : overbeek 1.3
69 :    
70 :    

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