SeWeR: PCR
Author: Malay

Select the program of choice. Paste your query in the query box. Click Submit button to pass on the query with default options. Please note that some programs might have some options/parameters that are required. Also note that SeWeR doesn't check whether the required option(s)/parameter(s) is supplied or not. See program description for details. Click Options button to fill up options. The button is a toggle. Clicking it again will close the option. Click Customize to customize this search. Fill up all the options that you require, then click Customize. SeWeR will open another window with a customized page. Save that file on your computer. Click Help to check the help page of the selected program. SeWeR will open a new window to show the help page. Click Submit to pass on the query. SeWeR will open a new window for results.
| Home | NucleicAcid | Protein | Database | PCR | Alignment | Tools | Bookmarklets | Customize Copyright © 2000 Malay Kumar Basu Send your comments/suggestions/bug-report to me: curiouser@ccmb.ap.nic.in Disclaimer

primer3
Mispriming Library (repeat library)
Pick left primer or use sequence
Pick hybridization probe or use oligo
Pick right Primer or use sequence
Sequence Id (a name to identify your sequence)
Region the primers will flank Formats: [base number],[number of bases] e.g. 50,2 or mark the sequence with []
Excluded Region Formats:[base number],[number of bases] e.g. 401,7 68,3 or mark the sequence with <>
Product Size Min Opt Max
Number of Return | Max 3' Stability
Max Mispriming | Pair Max Mispriming
General Primer Picking Conditions
Primer Size Min Opt Max
Primer Tm Min Opt Max | Max Tm Difference
Product Tm Min Opt Max | Primer GC% Min Opt Max
Max Self Complementarity | Max 3' Self Complementarity
Max #N's | Max Poly-X
Inside Target Penalty | Outside Target Penalty
First Base Index | CG Clamp
Salt Concentration | Annealing Oligo Concentration
Liberal Base | Show Debuging Info
Other Per-Sequence Inputs
Included Region to pick primers Format: Starting Base number, length e.g. 20,400 or mark the sequence with{}
Start Codon Position
Sequence Quality
Min Sequence Quality | Min End Sequence Quality
Sequence Quality Range Min | Sequence Quality Range Max
Objective Function Penalty Weights for Primers
Tm | Lt: |  | Gt: |
Size | Lt: |  | Gt: |
GC% | Lt: |  | Gt: |
Self Complementarity |
3' Self Complementarity |
#N's |
Mispriming |
Sequence Quality |
End Sequence Quality |
Position Penalty |
End Stability |
Objective Function Penalty Weights for PrimerPairs
Product Size | Lt: |  | Gt: |
Product Tm | Lt: |  | Gt: |
Tm Difference |
Any Complementarity |
3' Complementarity |
Pair Mispriming |
Primer Penalty Weight |
Hyb Oligo Penalty Weight |
Hyb Oligo (Internal Oligo) Per-Sequence Inputs
Hyb Oligo Excluded Region
Hyb Oligo (Internal Oligo) General Conditions
Hyb Oligo Size: | Min | Opt | Max
Hyb Oligo Tm: | Min | Opt | Max
Hyb Oligo GC% | Min: | Opt: | Max:
Hyb Oligo Self Complementarity
Hyb Oligo Max 3' Self Complementarity:
Hyb Oligo DNA Concentration
Hyb Oligo Salt Concentration:
Hyb Oligo Min Sequence Quality
Hyb Oligo Mishyb Library
Hyb Oligo Max Mishyb:
Hyb Oligo Max Poly-X: Max #Ns
Objective Function Penalty Weights for Hyb Oligos (Internal Oligos)
Hyb Oligo Tm Lt: Gt:
Hyb Oligo Size Lt: Gt:
Hyb Oligo GC% Lt: Gt:
Hyb Oligo Self Complementarity |
Hyb Oligo #N's |
Hyb Oligo Mishybing |
Hyb Oligo Sequence Quality |

codehop
Core (degenerate 3' region)
Degeneracy | Strictness
Clamp (non-degenerate 5' region)
Temperature | Poly-nuc
Primer concentration [in nM]
Codon usage table
Show the least degenerate, or show all overlapping primers
Use core strictness for the 3' base
Force the core/clamp boundary to be a codon boundary
Use the most common codons in the clamp

Primer3 |
Create PCR primers and Hybridization oligos from a DNA sequence. Input, DNA sequence. Required option-field, none.

CODEHOP |
Pick primers from multiple alingnment of protein sequences. Input type, BLOCKS. Required option-field, none.