Primer Nerd

 

Batch primer design for Fluorescence Polarization (FP) experiments. 

It would also work for other experiments requiring amplification primer pairs and single-base extension (SBE) primer.

The PCR primer pairs were designed with Primer3 (Steve Rozen, Helen J. Skaletsky (1996,1997,1998) Copyright (c) 1996,1997,1998 Whitehead Institute for Biomedical Research.)

 

1. Please give me the FASTA format sequence containing the SNPs specified by brackets (example).

 Analysis raw data: Primer3 output

                               Detailed extension primer design data

                              

2. The Amplification primers and extension primers will be emailed to you at

 

choice of output in gzip compressed format:

 

 

To do single PCR primer pair analysis, you may use Primer3 web interface to do a "more-choice" design.

Here we process analysis on a batch of sequences.  And currently only one pair of primers would be returned for each amplicons from Primer3 analysis.

 

Default parameters used:

For amplification primer design:

PRIMER_PICK_ANYWAY=1
PRIMER_NUM_RETURN=1
PRIMER_PRODUCT_SIZE_RANGE=80-150
PRIMER_MIN_TM=55
PRIMER_MAX_TM=70
PRIMER_MAX_POLY_X=4
PRIMER_MAX_DIFF_TM=10
PRIMER_PRODUCT_OPT_SIZE=90

For extension primer design:

        Oligo MW

        GC% (optimal 40 - 60%)

        Tm value (optimal 65- 85 C)

        Free energy of secondary Structure at internal, 3' end, and 3'end interacting with template compare to free energy of a specific primer-template binding

        PolyN (A, T, G, C, >4) penalty

 

To understand how to read the output of the program will refer to the readme file