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Revision 1.2 - (download) (as text) (annotate)
Wed Mar 3 12:49:23 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
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Branch point for: Branch-bobdev_news
Changes since 1.1: +6 -6 lines
fixes from DOE meeting

<h1>Assignments, Rules, and Checkboxes</h1>
To understand the way asssignments and creation/editing of translation rules work, you need to know 
the following:
<ol>
<li>
Functions assigned to genes can be either <i>translated</i> or not.  There is a link near the start of the page
describing a PEG (protein-encoding gene) where you can flip this option.  Your version of the seed has a <b>function.synonyms</b> table 
that contains the current translation rules.  If translation is in
effect, this table is checked for each function to see if it should be
translated to the accepted form before displaying it.
<li>
In the display of similarities you have check boxes corresponding to a
set of sequences (the gene you are examining plus each of the genes
for which similarity was detected).  Each gene has two check boxes:
<ol>
<li>
The first is the <b>ASSIGN to/Translate from</b> check box.  It is
used to select a set of sequences.  The selected sequences will be
either assigned a new function or will be used to construct new
translate rules.  You can select as many as you wish.
<li>
The second set of check boxes (actually, radio buttons, since you can
select only one) is for picking a single function that will be either
assigned to all sequences in the first set or will be used as the
function to which the others are translated.
</ol>
<li>
If you need to use the check boxes to make one or more assignments,
check the boxes on the left (the <b>ASSIGN to/Translate from</b> ones)
to pick the sequences that will be assigned a new function.  Pick the
single function you wish to assign to them by picking a single
<b>ASSIGN from/Translate To</b> entry.  Then click on
<b>Assign/Annotate</b>.
<li>
If you wish to add one or more translation rules, 
check the boxes on the left (the <b>ASSIGN to/Translate from</b> ones)
to pick the functions you wish to translate.  Pick the
single function you wish to translate to by selecting an
<b>ASSIGN from/Translate to</b> entry.  Then click on
<b>add rules</b>.  A note of caution: translations should be from a
function to a completely equivalent function (since the rule will be
applied to all genes); <b>do not pick a rule that would, for example,
translate TRANSPORTER to BRANCHED CHAIN AMINO ACID TRANSPORTER</b>,
since that would map all sequences with a function of TRANSPORTER to a
more specific function (which might well be accurate in the case you
are looking at).
<li>
If you have added or detected rules that should be eliminated, just
pick a single sequence from the <b>ASSIGN from/Translate to</b>
entries and click <b>check rules</b>.  You will then have the option
of removing any of the rules that translate to the chosen function
<li>
Finally, the given gene has two selection boxes, as well.  They occur
before the main table showing similarities.
</ol>
Good luck; we will undoubtedly redo this whole interface multiple
times, but for now this is what you get.


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