| Reverse Complement: Determines whether the primer reverse complements are output. Primers remain ordered from beginning to end of sequence. |
Yes No |
Space Between Plates: Determines whether the primers are output in a continuous stream, or interrupted by a blank line between plate contents. |
Yes No |
| Emit: Controls whether the output oligo list (and spreadsheet, if selected) iterates across rows or down columns. Does not change the layout of primers in the plate. |
Rows Columns |
Oligo Case: Determines whether the primers are upppercase or lowercase. |
Lower Upper |
| ResiduesLeave blank if all residues should be scanned. Otherwise, enter a list of peptides in their order of appearance in the sequence, one per line or separated by commas, or enter numbers or ranges of numbers, e.g. 4,13,46-59, one per line or separated by commas. If an offset should be applied to all numbers, enter this after a colon, e.g. 46-49,73-100:+5 means 51-54,78-105. The colon can also be used with an otherwise empty field. |
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Plate Layout: Determines whether the primers are organized in either: (1) columns of 8 and rows of 12; (2) 5 residues x 19 positions with one blank well (20 x 19 with 4 blank wells in 384 well format); (3) in groups of 8 and 12 with rows of 3 x 8 or 2 x 12; or (4) with each residue at the same relative position in a plate containing only primers of the same substitution (e.g., all A, all D, etc). |
8x12 5x19
all row aa by plate |
| Plate Numbers: Controls whether plate numbers are displayed before the primers. |
Yes No |
Wells/Plate: Specifies the number of wells per plate. |
96 384 |
| 5' Flanking Triplets: Specifies how many triplets flank the codon that is being replaced. |
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3' Flanking Triplets: Specifies how many triplets flank the codon that is being replaced. |
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| Excel File: Determines whether an Excel file with the primers is created. Each plate is placed in a separate worksheet. |
Yes No |
Spreadsheet Top Row: Allows the top row of the spreadsheet worksheets to be something other than 1. |
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| Well/Plate/Name Order Enter the order in which the well location, e.g. A1, (W), plate number (P), row letter (R), column number(C), oligo name (N), oligo sequence (S) or blanks (B) should appear. Delete letters to suppress corresponding information. Blanks can be duplicated. Delete all for oligo sequence only. |
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Codon Source: Specifies the source of codons. The preferred codon is given except in the case of the stop codon. Click "custom" to enter desired codons or show the preferred codons for the previously selected codon class. |
coli mammalian custom |
| Panel of 8: Lists the amino acids to be tested in the format in which rows are amino acids and columns are sequence locations. |
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Panel of 12: Lists the amino acids to be tested in the format in which rows are sequence locations and columns are amino acids. |
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| Panel of N: Lists the amino acids to be used to replace the original codon. For a single residue scan, e.g. Ala, enter a single letter. |
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Suppress Original: "Skip" means there will be no well (no oligo listed) for the original amino acid; "Blank" means there will be an empty well (blank line in the oligo listing); "Stop" means there will be a well with the designated stop/special codon. |
No SkipBlankStop |
| Codons: |
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Codons: |
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| Codons: |
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Codons: |
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| Stop Codon: Termination/21st codon |
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text |
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| Preferences: The save button allows the present values of the form to be stored (including codons). The reset button restores the page defaults without changing the stored preferences. |
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Saved Preferences: Remove any saved preferences without changing the values entered in the form. |
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