Team:NYMU-Taipei/synthoprime

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Revision as of 00:26, 29 October 2011 (view source) BarryChen (Talk | contribs) (→HOWTO: User Inputs) ← Older edit		Revision as of 00:27, 29 October 2011 (view source) BarryChen (Talk | contribs) (→Introduction) Newer edit →
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	==<font size=5><font color=crimson>'''Introduction'''</font></font>==		==<font size=5><font color=crimson>'''Introduction'''</font></font>==
-	*<font size=5>[http://120.126.44.58/SynthoPrime/ SynthoPrime] – A Synthetic Biology Primer Design Tool for Genomic Parts Creation</font>	+	<font size=4>[http://120.126.44.58/SynthoPrime/ SynthoPrime] – A Synthetic Biology Primer Design Tool for Genomic Parts Creation</font>
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-	*<font color=red>[http://120.126.44.58/SynthoPrime/ SynthoPrime]</font> 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. <font color=medium blue>It provides an automated ONE-STEP primer design service</font> of BioBricks for iGEM. <font color=medium blue>Near 1,400 bacteria and their 2,551 replicons (chromosomes and plasmids) are extracted</font> 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. <font color=medium blue>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.</font> [http://120.126.44.58/SynthoPrime/ SynthoPrime] is freely available for everyone to try out.	+	<font color=red>[http://120.126.44.58/SynthoPrime/ SynthoPrime]</font> 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. <font color=medium blue>It provides an automated ONE-STEP primer design service</font> of BioBricks for iGEM. <font color=medium blue>Near 1,400 bacteria and their 2,551 replicons (chromosomes and plasmids) are extracted</font> 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. <font color=medium blue>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.</font> [http://120.126.44.58/SynthoPrime/ SynthoPrime] is freely available for everyone to try out.
	==<font size=5><font color=crimson>'''HOWTO: User Inputs'''</font></font>==		==<font size=5><font color=crimson>'''HOWTO: User Inputs'''</font></font>==

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Revision as of 00:27, 29 October 2011

• Home Get to HOME
• Idea Our Idea
  Concept Brainstorming Background Review
• Design/ Experiment
  Optomagnetic Design Protein Modelling NeuroSymbiosis Chassis SynthoPrime Lab Protocol
• Results
  Optomagnetic Bacteria NeuroSymbiosis Chassis Parts International Collaboration
• Human Practice & Safety
  Synthetic Neurobiology Human Practice Evaluation & Safety Assessment
• About Us
  The School The Team China Meetup Acknowledgement

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.

HOWTO: Output Reading

Main output page

Additional Info.

References and Feedback

We would be more than happy to receive your comments and suggestions.