View source for FeatView

[[Image:FeatView home.png|thumb|right|600px|FeatView's homepage.]]
FeatView is CoGe's tool for finding genomic features by name or description.  

<font color=red>'''WARNING:'''</font> '''It is often difficult to find a [[genomic feature]] by name.'''  The main reason for this is the variety of names used for any given [[genomic feature]].  While CoGe can store multiple names for a given [[genomic feature]], only the names supplied in the original data file ([[dataset]]) are used.  If you are having difficulty finding a genomic feature by name, try to find the sequence for the feature and use [[CoGeBlast]] to search that sequence against the genome to which it belongs.

==Quick Start==
To use, just:
#Type in the name of the genomic feature in the "Name:" text box.
#Click on the "Search" button.
#Select the appropriate feature type.
#Select the appropriate genome for the feature.
#The annotation for the feature appears at the bottom of the screen.
[[image:FeatView At1g01010.png|thumb|right|600px|FeatView's results after searching for genomic features with the name "At1g01010".  The Arabidopsis thaliana genome from TAIR version 9 is selected and the feature type "[[CDS]]" is selected.]]
==Searching==
There are several options when searching for a genomic feature.  The easiest and fastest is if you know the full name of the feature and don't use any wildcards.  
===Searching by name===
Type in the name of the feature in the "Name:" text box.
===Searching by annotation===
Type in the annotation of the feature in the "Annotation:" text box.  By default, this search term has wildcards attached to both sides of the annotation.
===Using wildcards===
Wildcards can be added to either or both ends of a search term.  If a wildcard is not used, then only an exact match of the search term to the entire name or annotation will happen.  Otherwise, extra stuff can appear where the wildcard has been specified.  For example, searching for "protease" in the annotation without wildcards will only match features associated with an annotation that is "protease" and not "metalloprotease", "protease class II", or "metalloprotease class II".

<font color=red>'''WARNING'''</font>:  As currently implemented in CoGe, wildcard searching is slow.  Very slow.  So slow it is embarrassing.  If used, go for a long walk and get a cup of coffee.

===Why limit a search===
The more limits you place on a search, the faster it will run!  Definitely recommended if wildcards are being used.
  
===Limiting search by [[feature type]]===
You can limit your search to only features of specific type (e.g. CDS or gene).  The drop-down menu of feature types contains a list of all [[feature types]] currently in CoGe.

===Limiting search by organism===
You can search for an organism by name or description, and limit your search to only that organism.

===Running a search===
After the search criteria have been specified, just press the "Search".  The results will come back and be displayed below the search criteria box.  <font color=red>Warning:</font> this can take a while, especially if wildcards have been used.

=Annotation information and links for a selected genomic feature=
When a feature is selected, the full annotation of the feature is displayed.  This annotation box contains buttons which send the feature to other tools in CoGe, and a textual portion.  The textual portion displays [[annotation information]] about the genomic feature and contains additional links.
==Buttons==
===Get Seqeunce===
==In annotation links==
==Why are there sometimes multiple annotations?==
Multiple annotations are shown if there are multiple features of that type in that genome with the same name.  All of these get displayed right after one another.  A common case that causes this is when there are multiple splice variants of a gene, all of which share the same name