Overview:
This is the public target list that scientists are currently performing research on. The only difference between this target list and the proposed target list is that not every protein sequence in the proposed list will be investigated further. In this JCSG target list, every protein sequence will be researched. Click anywhere on the following target list table for a description of each column.
How to use Target List:
- Using the Page Slider:
As seen above, the target list contains many records (over 4,300 at the time of this writing) shown 60 records at a time. A handy slider is located in the upper-middle portion of the page, below the JCSG main logo. Clicking in the middle of the slider moves to a record between 1 and 4,300. Additionally, clicking on the left or right arrow once will bring you back or forward 60 records.
- Using the Target List:
Click on any area of uncertainty above to get a description of each category.
- Explanation of the Pictures/Icons:
Click on the picture for a more descriptive explanation of each.
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The particular protein sequence is already located in the Protein Data Bank.
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Information is known about similar protein sequences that a predicted structural model of the target list sequence can be made.
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Human homolog exists, meaning the target list sequence is similar to human protein sequence.
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- Sorting/Ordering the List
Clicking on the Species, Sequence ID, or Accession No columns will order the entire targets list based on that category alphabetically (from A through Z). All three ordering options are located on top of every column in the color blue. For example, clicking on the "Sequence ID" will sort the entire target list based on the sequence id.
Also, if the Accession Number is present and colored and underlined in blue, click on it. Clicking on it will bring a detailed Protein Sequence Comparative Analysis (PSCA) of the particular target. The PSCA contains the number of amino acids, PFAM Domain representations, secondary structure features, similarity of PDB Fold Assignment, and much more, in a graphical and friendly manner. Below is the PFAM display, which shows which domains overlap with one another. Single domains are shown in
brown () while overlapping domains are multi-colored ().
- Using the Filtering Tools:
The above sorting functions are located at the very bottom of each page of 60 records. Each category (ie "Select Species" or "Select Target Stage") can be combined to form a very specific filter which will only find a couple of results.
Select Species:
The "Select Species" box allows you to click on either Thermotoga Maritima or C. elegans category. Clicking once on C. elegans and clicking on "Filter Targets" will make the target list only display targets of species C. elegans. If you accidentally clicked on C. elegans, but wish to undo your click, press Ctrl on your keyboard and click on C. elegans again at the same time. The blue box highlighting the selected species will disappear.
Select Target Stage:
Click on the target stage to select a stage you wish to view in depth. For example, clicking on the "Crystal" stage will display all targets that have been crystalized, in addition to targets that have been produced beyond the Crystal stage (ie Data Set, Structure, and PDB), but will not display any targets below Crystal (ie Purified, Expression, Cloning, PCR, and Active).
Clicking on multiple stages (which is done by holding the Ctrl key on your keyboard and clicking once on the wanted stage) will display everything beyond that stage, in addition to everything that has currently at both stages.
If you selected the wrong stage and wish to undo your selection, simply click on a different stage. Additionally, if you did not wish to filter by target stage, use the "Ctrl and click" to remove any highlighted boxes.
Filter by Residue, Molecular Weight, Isoelectric Point, Methionine, Cysteine, Gravy:
The filters act like a math "greater than or equals" and "less than or equals" statement. It will retrieve any values that are within the defined range (ie. 6 x 10 will find values 6, 7, 8, 9, and 10). By filling numbers on both sides of the filter boxes, all targets that fall into that range will be displayed (as seen below). Additionally, clicking on the "Show Molecular Weight, Isoelectric Point, etc" check box will display the length or size of each wanted type after filtered (the filter will still work if you do not check that box, but the lengths will not be shown).
For example, entering the number of residues to be between 314 and 343
will show all targets with a length between 314 and 343. Clicking on "Show start-end residues" box will display the start and end sequences after being filtered. If that box is not checked, the target list will still be filtered correctly based on desired residues, but the start-end residues will not be displayed.
Definitions for Residue, Molecular Weight, etc can be found below:
- Residue
- Cysteine
- Gravy
Search By Description:
Search for a particular description by typing text into the "Search Description" box. In the example below, oligopeptide is typed in the box, meaning the filter will only show targets with oligopeptide as a description. Additionally, the "Show Description" box is normally checked, meaning a description will be shown after the filter for every target. If the box is unchecked, no description will be shown.
- Filtering the Targets:
Once all the criterias that you wish to filter by have been selected, click on the "Filter Targets" button. The page will be refreshed, with the targets that passed the filter displayed. Clicking on the "Reset" button will only clear all filtering boxes, in addition to the species and target stage boxes.