To record the details of a DNA Target in PiMS:
  click New DNA Target from the Target Functions page.   or select 'Create New DNA Target' from the Target menu




Then click New DNA Target towards the bottom of the Record New Target page.

New DNA Target form

• The 2 fields labelled 'Name' and 'Sequence name' are mandatory -as indicated by the *
  
  
• PiMS will provide a unique six digit number for the Target Name* 000001 in the example
  You may change this to a more meaningful name but it must not be the name of an existing Target in PiMS.
  note: this name will prepended to the identifier for any Construct records you create for this Target
    see Recoding a Construct for a DNA Target
  
    If the name you enter is not unique you will see the following warning:
  
  
  
• You may enter a GI number to identify an entry for the target in the GenBank database. PiMS will use this value to create a link to the record.
  
  
• Select an Organism from the list.
  The list contains the names of commonly used model organisms. These are provided as Reference data in PiMS. If the name of the Organism you wish to use for your Target record does not appear in the list, please contact your PiMS administrator who will be able to update the Reference data.
  
  
• The Function description field is used to categorize the type of DNA element the Target represents.
  Select a value from the list of: Intron, Promoter, Enhancer, 5'-UTR, DNA, genomic DNA, non-coding region and CRM.
  You may change this after the target record has been created.
  
  
• Select a value from the Project list -the list only includes the names of Projects which you are able to use.
  
  
• By default the Scientist field displays the name recorded for the user who is currently logged in. -Demo PiMS in the example
  You may change this by selecting a different name from the list.
  
  
• Any additional details can be recorded in the Comments field.
  
• Enter a DNA sequence for the Target
  note: if you wish to record details of any Constructs for this Target, the sequence must be ≥50 nucleotides long.
    see Recoding a Construct for a DNA Target
  
  
• When you have completed all of the mandatory fields click the button.
  The Target information will be recorded and displayed in a PiMS DNA Target details view.
  
  

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The DNA Target Details View is displayed after clicking the button when you record a new DNA Target in PiMS.
You can also see the details for a DNA Target when you:
  -click the magnifying glass icon next to the record in the results from a 'Target Search' or the 'Browse Targets' page.
  -select 'View' from the context menu for a DNA Target record in the 'History' brick on the PiMS Home page.

The Target details view page includes an icon, identifying the view as a PiMS Target, a link to a list of all Targets in PiMS, and updatable information, about the individual Target, in a series of PiMS boxes.

Target details as recorded

• The first box, which is open by default, includes the Target names, source organism, function, the name of the scientist responsible for the Target and any additional comments.
  If you have permission to edit the Target details, you will see Make Changes... at the bottom right hand side of the box. -this is not displayed in the example
  
  
• Open the box labelled DNA Sequence to see the Target DNA sequence.
  The length and % of GC nucleotides in the sequence are also shown.
  Click Fasta pop-up to see the entire Target DNA sequence in Fasta format.
  
  
  
  

Target-related Information

The lower part of the DNA Target Details View contains additional information about the Target.
This includes details of any Constructs, Experiments and Database references which may have been recorded for the Target.


• Details of any Constructs which have been recorded for the Target will appear in the box labelled 'Constructs'.
    -there are no Constructs recorded for the Target in the example.
  
  
  
• Click New Construct to record the details for a Construct. -see Recoding a New Construct for a DNA Target
    note: It is not possible to record Construct details if the DNA sequence is <50 nucleotides long.
    This will be indicated by the following message:
  
  
  
• Database References for the Target are listed in the box labelled 'Database references'.
  
  Click the link in the 'Accession' column to view the web page.
    -the example shows a link to a GenBank reference created from the value entered for the GI number when the Target details were recorded in PiMS.
  
  
• Open the Box labelled 'Blast searches' then click EMBL Blast results to see the results of a Blast search against the EMBL database.
    -see Blast help for more details.
  
  
• The boxes labelled 'Images' and 'Attachments' allow you to associate images, with legends, and other files with the Target.
  
  
• The box labelled 'Notes' is to record any additional details about the Target. Each note is saved with the date it was recorded allowing you to track any changes made to the Target detals.

To record a new 'Construct' for a DNA Target either:
  -click New construct on the Target Details page
  or:
  -select  New Construct... from the 'Context menu' for a DNA Target in the 'History' brick on the Home page.

You will see Step 1 of the New DNA Construct wizard.

New DNA Construct Step 1: Basic details

The DNA Target sequence is displayed along with a form to define the region of the sequence to be used for the Construct.

• Enter the start and end nucleotides for the Construct.
  By default these are the first and last nucleotides in the DNA sequence. 1 and 576 in the example
  
  
• Enter an identifier for the new Construct; this will be appended to the Target name to create the Construct Name
  
  
• Click to proceed to Step 2.
  If you enter unsuitable values for the start and end nucleotides you will see an appropriate warning:
  
  
    if you enter a value < 1 for the start nucleotide
  
  
    if the Construct id value has already been used for a Construct for this Target
  
  
    if the start nucleotide position is > the end nucleotide position
  
  
    if the length of the selected region is < 50 nucleotides
  
  

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New DNA Construct Step 2: Select Primers

Step 2 displays 3 PiMS boxes.
The first contains the Target DNA sequence.

The second, labelled 'Basic details from Step 1 for:' contains the Construct Id, generated from the Target Name and the id value entered in Step 1  -in the example this is 000918.con1,
and the Start and End nucleotides defined in Step 1  -in the example these are 145, 500.

It also shows that a default value of 60°C is used to design Primers for the Construct.

Below this is the Construct DNA sequence.



The third box contains a list of suggested Forward and Reverse Primers:

• If there are no suitable primers enter a different Primer design Tm value and click to see updated lists.
  
  
• Click the radio buttons to select 1 Forward and 1 Reverse primer then Click to proceed to Step 3
  
  
• Click or the Browser back button, to return to Step 1
  
  

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New DNA Construct Step 3: Primer Extensions

Step 3 displays 4 PiMS boxes. These contain the "Target DNA sequence" and the "Basic details from Step 1".

The third box displays the details of the primers selected in Step 2 including: the sequence, length, Tm and % of GC nucleotides for the Forward and Reverse primer.

The fourth box, labelled "Primer 5'-Extensions" includes drop-down lists of 5'-extensions for the primers.
  note: the 5'-extensions are PiMS Reference data.
You can see a complete list of all the 5'-extensions in PiMS by clicking Extensions List

• Click in a box to see the list of available 5'-Extensions for the Forward or reverse primer.
  
  
  
• Select a 5'-Extension to add to your primer sequence
  
  
• or select 'none' if you do not wish to add a 5'-Extension to your primer.
  
  
• If the list does not contain a suitable sequence, select *Record a new 5'-extension*
  You will see two new fields to enter a Name and Sequence for a new 5'-Extension for the Forward or Reverse primer.
    -the example shows the fields displayed for recording a new Forward primer extension
  
  
  
• When you have completed your selection click to proceed to Step 4
  
  
• or click or the Browser back button, to return to Step 2.
  
  

New DNA Construct Step4: Construct Summary

Step 4 displays 4 PiMS boxes.
These contain the "Target DNA sequence" and the "Basic details from Step 1".

The third box displays the "Primer details and properties".
This includes the Length, Tm and %GC for the both the complete sequence and the gene-specific region, or 'Overlap', for both the Forward and Reverse primers. The sequence of any '-extension is also shown.



The fourth box contains a form for recording some additional details:

• You may enter a short Description for the Construct.
  More details can be entered in the Comments field
• Select a Person from the drop-down list -the name of the user who is the currently logged in user is selected by default
• Click to create a new Construct record in PiMS or Click the button, or the Browser back button, to return to Step 3
  
  

Clicking takes you to Constructs table on the parent Target details View


The Table includes the Construct Name, derived from the Target name and the Construct ID   - '000918' and 'con1' in the example
and any description entered in Step 4   - 'Novagen EK/LIC' in the example.

The Construct details view is displayed when you:
  -click the link in the 'Construct Name' column in the Constructs table on a DNA Target details View
  -select a 'Construct/Target' link from the History menu
  -select  View from a Construct context menu in the 'Constructs no progress' or 'History' brick on the PiMS Hone page.


The Construct Details View includes:

•   Sequences of the entire Forward & Reverse Primers, the Gene-specific region and any 5'-Extension
  
  
•   The Length, Tm and %GC for the entire Forward & Reverse Primers and the Gene-specific region
  
  
•   Predicted PCR product sequence, length and %GC
  
  
•   Editable of a Description and Comments fields
  
  
•   A link to the PiMS record for the Scientist responsible for the Construct