Team:NYMU-Taipei/synthoprime

From 2011.igem.org

Slide Down Box Menu with jQuery and CSS3

1 Introduction
2 HOWTO: User Inputs
3 HOWTO: Output Reading
4 References and Feedback

Introduction

[http://120.126.44.58/SynthoPrime/ SynthoPrime] – A Synthetic Biology Primer Design Tool for Genomic Parts Creation

[http://120.126.44.58/SynthoPrime/ SynthoPrime] algorithm is developed to provide the access of all the available genomic parts (biological parts from sequenced genomes) for the specific needs of primer design in synthetic biology communities. It provides an automated ONE-STEP primer design service of BioBricks for iGEM. Near 1,400 bacteria and their 2,551 replicons (chromosomes and plasmids) are extracted from NCBI genome database by BioPerl package as genomic templates in our service. The jQuery Javascript library is used for interactive web user interface design to help synthetic biologists to access genomic parts from the sequenced genome templates for primer design. Our online service aims to provide a one-step primer design tool and sequenced genomes as templates to convert sequenced genomes into biological parts with quantitative measures for synthetic biology community. [http://120.126.44.58/SynthoPrime/ SynthoPrime] is freely available for everyone to try out.

HOWTO: User Inputs

STEP 1: Offer your sequence to be ‘biobricked’ by direct pasting your DNA or specifying by names of organism, replicon and gene.	STEP 2: Give your design constraints for primers, including length, melting temperature, GC-content of each primer and differences of Tm between forward and reverse primers. The primer selection process is powered by primer3.
STEP 3: In addition, you can choose to relax design constraints to gain more primer candidates. Besides, you can decide to put prefix or suffix or not by ‘Build Biobrick’ checkbox and specify extra bases before prefix and suffix for good enzyme digestion!	STEP 4: Click “SEND” when everything is ready or click “RESET” to set all parameters as default.