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<h1>An Explanation of the SEED Evidence Codes</h1>

Within the SEED, we use evidence codes to reflect significant factors
that go into making assignments of function.  Some of these codes are
computed and reflect information that we consider particularly
useful.  Others are used to reflect experimental evidence of function.

<h2>icw(n): in cluster with</h2>

This code indicates that the PEG occurs in a cluster with <i>n</i>
other genes from the same subsystem (very strong evidence).  There may
be several of these for a PEG (up to one for each subsystem the PEG
occurs in).

<h2>isu: in subsystem unique -- the only entry in a subsystem cell</h2>

This code indicates that the PEG occurs in a subsystem, and it is the
only PEG for that genome that has been assigned the functional role
(i.e., the cell in the spreadsheet contains a single entry).  This
means that, if you wish to change an annotation, you should discuss it
with the owner of the subsystem.

<h2>idu(n): in subsystem duplicates</h2>

This code indicates that the PEG occurs in a subsystem, but it is 
in a cell of the spreadsheet containing duplicates (and it is not
clustered with other genes connected to the same subsystem).
In this case, you may make a change without notifying the owner of the
subsystem, since you are probably disambiguating the situation to his
benefit.

<h2>ff: in FIGfam</h2>

This code indicates that the protein-encoding gene is included in a FIGfam.

<h2>cwn: Clustered with Nonhypothetical</h2>

This code indicates that the protein-encoding gene is functionally
coupled to at least one other protein that has been assigned a
function that is considered "nonhypothetical".  The functional
coupling score must be 5 or more for this code to apply.  This means
that the gene co-occurs on the chromosome in at least 5 instances of
genomes that are not close strains with another gene that is
considered nonhypothetical.

<h2>cwh: Clustered with Hypothetical</h2>

This code indicates that the protein-encoding gene is functionally
coupled to at least one other protein that has been assigned a
function, but none  that is considered "nonhypothetical".  The functional
coupling score must be 5 or more for this code to apply.  This means
that the gene co-occurs on the chromosome in at least 5 instances of
genomes that are not close strains with at least one other gene, but none that is
considered nonhypothetical.

<h2> dlit: Direct Literature References to the Gene Exist </h2>

This code is used to indicate that at least one paper (that is a
"nongenome paper" in the sense that it does not reference hundreds of
genes) is associated with this gene.

<h2> ilit: Indirect Literature References to the Gene Exist </h2>

This code is used to indicate that at least one paper (that is a
"nongenome paper" in the sense that it does not reference hundreds of
genes) is associated with a gene assigned the same functional role,
but none to this gene itself (as far as we know).




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