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the HOPSS stuff for the prototype web site

<h1>Help text for the field "Chose problem type" </h1>
<br>
<h2>Missing gene for a role</h2>
The presence of a functional role in an
organism is inferred, but the corresponding gene cannot be identified
by reliable homology projection. Genome context analysis techniques,
most notably clustering on the prokaryotic chromosome, may generate
candidate genes for a sought functional role.
<br>
<br>
<h2>Gene in subsystem without clear role</h2>
This includes genes that have been implicated
in a particular functional process but are still lacking specific
functional annotation.  For example, bioH has been known for years to
be important for biotin biosynthesis, however it's exact biochemical
role remained unknown.

<br>
<br>
<h2>Role out of context</h2>
This is appropriate when the presence of a gene assigned with specific
functional role cannot be justified by functional context analysis. In
some cases, this may reflect annotation/gene calling problem or merely
an incomplete subsystem coverage. However, in other cases such orphan
genes may lead to an inference of novel reactions and processes.

<br>
<br>
<h2>Missing input/output</h2>
Used to reflect the situation when the origin of a
substrate or utilization of a product is unclear and cannot be
reconciled with an existing biochemical knowledge captured in a
subsystem. In some cases these observations may lead to the inference
of a novel gene or pathway.

<br>
<br>
<br>
<h2>Functionally coupled hypothetical</h2> 
In many cases genes with unknown
functions appear to be strongly functionally coupled with a subsystem
via chromosomal clustering and other types of evidence provided by
genome context analysis. A detailed subsystem analysis may help to
suggest a specific function for this hypothetical.

<br>
<br>
<h2>Orphan chromosomal cluster</h2>
Genes that tend to co-localize on the
chromosome in phylogenetically distant prokaryotes are often
functionally related.  Chromosomal clustering of hypothetical genes in
combination with other types of evidence may lead to identification of
a novel biological pathway.

<br>
<br>
<h2>Unresolved paralogs</h2>
Multiple genes associated with a single
functional role (paralogs) may indicate incorrect annotations.  In
some cases these inconsistencies can be resolved based on genome
context analysis


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