By default, the Customize Results subpage of the processing method editing wizard is inactive. To edit the parameters on this page, select the Enable Customize Results checkbox.
IMPORTANT
The Enable Customize Results checkbox can only be selected if an appropriate ribonuclease was previously selected on the Identification subpage of the processing method editing wizard.
The ribonuclease options "Nonspecific" or “None” are not supported for theoretical digestion at this time. Do not use these ribonuclease options if you want to enable the Customize Results subpage.
The Customize Results subpage includes three sections: Theoretical Digestion and Alias Naming (editable), Ribonuclease Defined on Identification (read-only), and Theoretical Digestion and Alias Naming Results (populated after the Theoretical Digestion and Alias Naming parameters are entered and applied).
| No. | Description | No. | Description |
|---|---|---|---|
1 | Parameters tab (processing method editing wizard) | 5 | Theoretical Digestion parameters |
2 | Subpage navigation bar | 6 | Ribonuclease Define on Identification |
3 | Enable Customize Results checkbox | 7 | Apply button |
4 | Alias Naming table | 8 | Theoretical Digestion and Alias Naming Results table (shown blank) |
The table below describes the parameters on the Customize Results subpage.
Parameter | Description |
|---|---|
Enable Customize Results (checkbox) | Select the Enable Customize Results checkbox to activate the Customize Results page and assign theoretical digestion and alias naming parameters to the currently open processing method. |
Theoretical Digestion and Alias Naming | |
Theoretical Digestion and Alias Naming (table) | A custom naming scheme (up to 50 characters) can be entered into the Custom Chain Alias Root column of this table. The alias chain root is applied as a naming scheme for the oligonucleotide components identified in the analysis. |
Digested Sequence Length Constraints | Specifies the upper and lower limits of the length of the theoretical digested oligonucleotide sequences.
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Theoretical Digested Sequence Mass Range | Specifies the upper and lower limits of the masses of the theoretical digested oligonucleotide sequences.
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Number of Allowed Missed Cleavages | Specifies the maximum number of internal cleavage sites within a oligonucleotide that the ribonuclease might miss during the digestion process.
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Ribonuclease Defined on Identification | |
RNase | Read-only. Specifies the RNase assigned to the processing method on the Identification subpage of the processing method editing wizard. |
Custom Specificity | Read-only. Specifies any custom specificity (if applicable) of the RNase assigned to the processing method on the Identification subpage of the processing method editing wizard. |
Phosphate Location | Read-only. Specifies the phosphate location defined for the processing method on the Identification subpage of the processing method editing wizard. |
Once you enter the Theoretical Digestion and Alias Naming parameters and select the Apply button, the results of the theoretical digestion appear in the Theoretical Digestion and Alias Naming Results table on the right side of the page.
The table below describes the information in the Theoretical Digestion and Alias Naming Results table.
Column | Description |
|---|---|
Alias Name | Displays the name of a theoretical digestion component using the alias root defined in the Theoretical Digestion and Alias Naming table. For example, if “Chain1” was typed into the Custom Chain Alias Root column of the Theoretical Digestion and Alias Naming table, the theoretical digestion components listed in the Theoretical Digestion and Alias Naming Results table will appear as “Chain1_x”, where x indicates the theoretical component number. |
Selected Oligonucleotide Sequence Chain Name | Indicates the default name (derived from the FASTA file) of the oligonucleotide sequence assigned to the currently open processing method. |
Sequence | Displays the nucleotide sequence constituting the theoretical digestion component. |
Digested Sequence Mass | Displays the mass of the nucleotide sequence constituting the theoretical digestion component. |
Start Position/End Position | Indicates the positions of the first and last nucleotides of the theoretical digestion component within the undigested target oligonucleotide sequence. |
Sequence Length | Indicates the number of nucleotides in the theoretical digestion component. |
Nonunique Sequence | Indicates the number of times the oligonucleotide sequence appears in the theoretical digestion results |
Isomer Group | Indicates the group to which a particular series of isomeric oligonucleotide sequences belongs. |
Number of Isomer Sequences | Indicates the number of isomeric oligonucleotide sequences of a particular mass that appear in the theoretical digestion results. |
Miscleavage | Indicates the number of miscleavages (if any) involved in producing a theoretical digestion component. The values in this column are based on the Number of Allowed Missed Cleavage Sites parameter in the Theoretical Digestion and Alias Naming section of the Customize Results page. If the value in this column is 0, no miscleavages occurred to create the theoretical digestion component. |
Digest Position | Indicates the relative position of a particular nucleotide at which the theoretical digestion took place; based on the specific activity of the ribonuclease assigned to the theoretical digestion and intrinsically related to the theoretical component number listed in the alias name. For example, since RNase A cleaves the internal phosphodiester bonds of cytosine (C) and uracil (U) bases, for a theoretical digestion using RNase A, a digest position of 3 indicates that the theoretical digestion component resulted from RNase A acting at the third C/U-containing nucleotide in the target oligonucleotide sequence. For alias root “Chain1”, this theoretical component would have the alias name “Chain1_3”. |