WebAGCoL User Documentation
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This document describes different features of the WebAGCoL Package and its tools.

CONTENTS OF WebAGCoL PACKAGE

  • WebFPC: A web based java program to view the contigs of FPC database.
  • WebChrom: A web based display to browse the chromosome for markers and contigs.
  • WebBSS: A web interface to BSS. BSS organizes sequence searches against target sequences which are located on an FPC map. The target sequences can be BAC-end sequences (BES) or sequenced clones.
  • WebFcmp: A web tool for fingerprint comparison.




WEBFPC [ Back ]

WebFPC allows the user to view the contents of a contig.


Contig Selection Screen [ Back ]

The Contig Selection Screen is divided into two sections: Select Contig on the left side and Search for Contig on the right. Both can be used to locate a contig for viewing.


Select Contig Area [ Back ]

 

The Select Contig section, seen in Figure 1 on the right, contains a list of contigs by their number with other useful information in the other columns. You can select a contig by double clicking on the row or by clicking on the row and clicking on the "Display" button underneath the list.

Going over the column headings from left to right, they are "Contig", the contig's number. The three in the middle are "Clones", "Markers", and "Sequenced"; the number of clones, markers, and sequenced clones, respectively, in each contig. The number of sequenced clones are those with a FINISHED status. Next is the Q number, which is the number of clones that FPC failed to place properly; it provides a good measure of the quality of the contig. Any contig with a Q number under 6 or so is a good contig. However, users should use their own judgment. A '-' character indicates that the Q number not known; it is not the same as a 0. Last is the "Chr" column, which contains the chromosome number if the contig has been located on a chromosome.

Figure 1: Selection AreaContig Select List


Search for Contig [ Back ]

The Search for Contig, seen in Figure 2, allows the user to search for a contig by the name of a marker or clone contained within the contig. To search, enter the clone/marker name in the text area next to the "Search by Marker" or the "Search by Clone" button, as appropriate, and then press enter or the Search button. The results will appear in the list box below. You can then display a contig by double clicking on the row containing the contig number.

Wild characters: To search for all markers with a given prefix, enter the prefix followed by a '*'. For example, the string 'R*' entered into the Marker box will list all markers starting with a 'R'. Figure 2 shows that entering the '*' lists all markers. If a name is entered without any preceding or trailing '*', yet the marker cannot be found, a '*' will be put on the beginning and end of the name and a new search will be done. These same rules apply to clone names.

The text in-between the buttons and the results list is used to report the status of searches. Messages appear at the top, and move down when others appear.

When a search is running, the search button will turn into a stop button, which should be pressed to stop the search. Also, the search will be automatically stopped when you select a contig.

The "Clear" button, located under the results list, clears the results list. Otherwise, the results of each consecutive search will be appended on the end of the list.

Figure 2: Search AreaContig Search Panel


Contig Display Screen [ Back ]

The Contig Display Screen displays the contents of a contig. Most of the screen in taken up by the display area, with the control section along the top.

Display Control Area [ Back ]

The Control Area is used to adjust the Main Display Area, and show some basic information regarding the contig.

Figure 3: Controls, Top Row
Controls

Back Button: Returns the user to the Contig Selection Screen.

Clone Rows: To change the number of clone rows, simply change the number in the text area next to the "Clone Rows" and press enter. If the number entered is greater then the number of clones visible, the new number of rows will be reduced to the number of visible clones.

Show Clones: The concept of "burying" a clone requires a little explanation. If FPC determines that two clones have similar fingerprints, one is buried within the other. The buried clone is referred to as a Buried or Child clone, while the clone into which it is buried is described as a Canonical or Parent clone. The type of burying reflects the degree to which the fingerprints agree, exact being the strongest, followed by approximate and then pseudo (see Table 3 also). The control has three settings;

  • No Buried: all buried clones are hidden, leaving only the canonical and normal clones.
  • All: all clones are displayed; canonical, buried, and normal.
  • Seq Only: only the sequenced clones are shown.

Remarks Choice

Figure 4: Remarks
Remarks

Clone Remarks 1 - click on it to hide the clone (primary) remarks
Marker Remarks - click on it to hide the marker remarks
Clone Remarks 2 - click on it to hide the clone (secondary) remarks

Zoom Controls

Figure 5: Controls, Bottom Row
Bottom Row

On the bottom row are the zoom controls. The text area next to the 'Adjust Zoom by' label contains the scale by which the zoom will be changed. It can be changed by clicking on it and then typing the new scale, pressing enter has no effect. The scale can be any positive decimal number or scientific notation that is greater then 1. For example; "2", "1.001", and "3.1415e3" are all valid values. To the right of that is the buttons that zoom the view in and out.

Linking to other sites
Figure 6: Other Sites
Information Lookup Control

Figure 6 shows the control for looking up additional information on the web. The Chooser box shown in Figure 6 is set by default to "No highlight". Pull-down on the box and it will show the web sites that this FPC project can link to. Select a web site, and all clones and markers that have information at that site will turn light-red. Select a light-red clone or marker and then click the "Link to Site" button to view the record at the corresponding site.

If you are interested in having WebFPC provide such a connection to your database, please contact us.



Main Display Area [ Back ]

The Main Display Area is divided into four sections: from top to bottom they are the marker, clone, remark, and anchor areas. If the Main Display Area is too large, the marker, clone, and remark areas are placed in a scrollable window panel. The anchor area is placed in a separate scrollable window panel. The horizontal scrollbar for the three upper areas is below the Anchor Display Area. Figure 7 shows the main display area; the four sections are labeled in red.

Figure 7: Main Display Area
Main Display Area


Selecting Clones and Markers [ Back ]

Clicking on a clone or a marker selects it. This is indicated by a cyan colored box around the selection. If there are other items, such as remarks or clones, that are associated with the selection, they are highlighted in green. See Table 1 for a list of items and their association. Selecting a Remark has the effect of selecting its Clone, so the Clone will be highlighted in cyan and the remark in green.

Table 1: Selection Highlighting Colors
Selected Item Associated Items
Marker
  1. All Clones that hit it.
    2.
Clone
  1. Markers the clone hits
  2. Clones which it is buried by.
  3. Clones that are buried by it.
  4. Remarks attached to it.
    5.


Clone Types [ Back ]

Clones that are in the process of being sequenced, or have been sequenced are highlighted when not selected. Table 2 list the different types and their colors (these are the defaults, and may be changed at installation). Figure 11 shows examples of all three.

Table 2: Shotgun Clone Colors
CloneType
 Color
Tiled Orange
Shotgun Grey
Sequence Completed Yellow

Figure 11: Shotgun Clones
Shotgunned Clones

Buried and Canonical clones are marked with a special character after their names. See Table 3 below for a list of the characters and their meaning. In Figure 11, above, clones a0063H01 and a0040B11 are both examples of "Canonical, All Types of Children" clones and are marked as such with a '*'.

Table 3: Clone Type Indicator Characters

Clone Type Character
Buried, Exact =
Buried, Approximate ~
Buried, Pseudo #
Canonical, Pseudo Children Only +
Canonical, Any *



The Anchor Area [ Back ]

The Anchor Area contains any genetic anchors in the contig. Clicking on an anchor moves the view to that region of the display.


Marker Filter [ Back ]

The users can filter and color the markers that they want to get displayed in the Main Display Area using these settings. Figure 12 shows the default filter settings. Each row in the table is a rule which specifies what markers are going to be displayed and in what color.

  • Type: denotes the marker's type; eg, STS, eMRK. '*' denotes markers of any type. Note that only the types of markers present in current contig are listed here.

  • Substring: This matches all the markers with this string as a substring in their name (eg. 'J99' or '*J99*' match 'OJ991018_02' etc) or prefix (eg. 'OJ99*' matches 'OJ991018_02' but 'J99*' doesn't match it) or suffix (eg. '*60' matches 'SOG0460'). '*' matches markers with any name.

  • Remark: This matches all the markers with this string as a substring in their remark (eg. 'rker' will match with the marker remark 'This is s Marker Remark').'* matches marker with ANY remark.

  • Color: This is the color with which a marker that satisfies Type and Substring and Remark will be colored with. 'INVISIBLE' denotes that the marker will not be displayed.

    • Figure 12: Marker Filter: Default
    Marker Filter

    To add a rule, click 'Click to Add' and a row gets added to the table. Use the Input boxes to make a rule. And then click 'Apply'. All the rules in the table are applied together; that is, a logical OR is taken of all the rules, with priority given to a rule which is lower down in the table. For each row, a logical AND is used to combine the entries in the row's columns.

    Example: The rule highlighted in black in Figure 13 would color all the markers of type 'eMRK' which have 'SOG' as a substring in their name with the color 'Orange' as shown in Figure 14. The default 3 rules also apply but the last rule takes precedence. Hence the markers that do not satisfy this rule are colored using default rules, and those which do satisfy it are colored with 'Orange'.

    Figure 13: Marker Filter: Add a Rule
    Marker Filter 1

    On Applying, the markers are displayed in the Main Display Area as shown in Figure 14.

    Figure 14: Main Display Area: Result
    Main Display Area 1




    WebChrom     [ Back ]

    WebChrom is a web based graphical display to browse the chromosome for markers and contigs of FPC database.


    Chromosomes (or Linkage Groups) Display     [ Back ]

    WebChrom graphics is generated from a FPC database. FPC allows contigs to be assigned to a position on a chromosome; such contigs are referred to as 'anchored' contigs. The Chromosome display shows the positions of each anchored contig.

    If there are sequenced clones that have been entered into FPC as simulated digest clones, the location of each clone is shown as a green line.

    Click on a chromosome to view the expanded view.


    Expanded view of a chromosome     [ Back ]

    The contigs and frameworks are shown ordered along the chromosome. FPC can contain a set of ordered markers, which are generally from a genetic or radiation hybrid map. These ordered markers are referred to as anchors. The well-ordered anchored are referred to as frameworks and the binned anchors are referred to as placements. Only the frameworks on shown on this display.

    The length of the contig corresponds to the the position of its corresponding frameworks. If two contigs overlap based on their frameworks, the algorithm computes the framework which is most likely to be wrong, and a yellow unbounded box is drawn to that framework. Hence, no 'bounded' yellow boxes overlap.

    Information for contig
    Put the mouse over a contig and click, a popup will display the following informations:
    View in WebFPC click this and it will display the corresponding contig.
    x - y cM x is the CB position of the first framework and y is the position of the last framework.
    n total clones the number of clones in the contig
    n sequenced clones the number of sequenced clones.
    n unique markers number of markers in the contig.
    Max CB value: n the length of the contig is in CB (consensus band) units, where one CB is approximately one restriction fragment. With agarose gels, a fragment is approximately 4096 bp, so multiply n x 4096 gives the approx length of the contig in bp.
    CB x - y covered by FWs: x is the CB position of the first framework and y is the position of the last.
    n framework(s) hit in the chr total number of framework.
    Also hit .... this lists if any of the frameworks that hit other chromosomes.

    Information for framework
    Put the mouse over a marker and click, a popup will display the following informations:
    View in WebFPC click this and it will display the corresponding marker in WebFPC. If the marker hits multiple contigs, a list of the contigs will appear, else the contig for the marker will be displayed.
    ... There may be links to other databases with information about the framework.
    Position x the cM position.
    Hit n the number of clones it hits on each contig that contains it.



    WebChrom Search [ Back ]

    WebChrom is a web based graphical display to browse the chromosome for markers and contigs of FPC database. WebChrom Search is a part of WebChrom and is designed to allow you to search by marker name, by marker remarks or by multiple combinations of the two to view the distribution.

    Quick Overview:
    • Step 1) Enter the marker name and/or remark into the top two boxes.
    • Step 2) Press the "Add it" button.
    • Step 3) Press the "Search (match All conditions)" button on bottom.
    Note: If a carriage return is entered after typing a name or remark, the search is automatically executed (i.e. as if you performed Step 1 and Step 2).

    Note: if you enter both a name and remark, the software will search for any marker with that name and remark. You can also enter just a remark or just a name.

    More Detailed Searching Rules:
    Specifying Marker Name or Remark: For either marker name or remark, you can type a substring. The rules are as follows:
    • An asterick at the beginning of a substring matches everything that ends with the substring.
      For example, *123 will match Locus123, STS123, etc.
    • An asterick at the end of substring matches everything that starts with the substring.
      For example, Locus* will match Locus123, Locus456, etc.
    • A blank or asterick matches all names or remarks.
    More Complex Searches:
    • You can create more complex searches by populating the search condition box with more than one marker name and remark to search on. That is, execute Step 1 and Step 2 any number of times before executing the search. Each combination of Name/Remark will be entered as one line in the scrollable box.
    • If your have multiple items in scrollable box, the bottom button titled "Search (match ALL conditions above)" will only display markers that match every single search line.
    • If your have multiple items in scrollable box, the bottom button titled "Search (match ANY conditions above)" will display all markers that match any single search condition line.



    WebBSS     [ Back ]
    WebBSS is a web interface to BSS. BSS organizes sequence searches against target sequences which are located on an FPC map. The target sequences can be BAC-end sequences (BES) or sequenced clones.

    Quick Overview:

    Step 1) Enter the sequence or Upload the sequence file you want to search against the target sequences.
    Step 2) Specify the BSS options for your search. (Refer to the section below for description of BSS options.)
    Step 3) Press the "Submit" button to start the search.

    Description of form fields:
  • Database Type: Two types of database are used with BSS searches BES and Genomic
    • BES: BES database contains BAC-end sequences
    • GENOME: GENOME database represent sequenced clones
  • Blast Expectation Value: The statistical significance threshold for reporting matches against database sequences; the default value is 50.
  • Query type: You must specify the type of sequence entered for as Marker/Sequence. Query type and database type determine the map used for bss search.
  • Additional Blast Parameters: You can also specify additional blast parameters that you want to use for the BSS search. More details on blast parameters can be obtained from NCBI BLAST help
  • Search Type: You can search the database for matches to All Contigs, or Single Contig, or Search for Contig Ends. If you are interested in searching for single Contig you have to specify the contig number that you want to search against. In case of Search type as Contig Ends you have to specify the distance from the ends that should be matched.
  • Output Option:
    • To web browser: Your job will run immediately and return results directly to your Web browser in HTML format.
    • By E-mail: The results will be sent within the body of email message, to the email address you entered.


    • WebFcmp [ Back ]

    WebFcmp is a tool to compare a FPC clone against all others clones.

    Quick Overview

    Step 1) Specify the cut-off value for the comparison results. The default value is 1e-10. Note: Lower value is more stringent
    Step 2) Specify the Clone name that you want to compare against FPC database. (Refer to the section below for selecting the clone names if not known)
    Step 3) Press the "Submit" button to start the search.

    Steps for selecting clones for comparison from FPC Database.
    • Select the library for which you want to obtain the clone names.
    • Next specify the plate number from which you want to obtain the clone names.
    • Then select the clones by checking the clones you want to compare.
    • Press the 'Enter selected' button to complete the selection steps. Note you can select all the clones for comparison from plate by using 'Select All' option and then press the 'Enter Selected' button.
    • Then press 'SUBMIT' to do the comparison.
    Email Comments To: www@agcol.arizona.edu