Team:NYMU-Taipei/synthoprime

From 2011.igem.org

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<!--- primerone --->
 
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SynthoPrime – A Synthetic Biology Primer Design Tool for Genomic Parts Creation
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==<font size=5><font color=crimson>'''Introduction'''</font></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. 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.
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<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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By using <font color=red>[http://120.126.44.58/SynthoPrime/ SynthoPrime]</font> program, you can <font color=dodger blue>design your own biobrick primers</font> by <font color=dodger blue>selecting genes</font> that you need with quantitative measures, including primer length, melting temperature and GC content.
 
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<font color=dodger blue>You can access any genes from sequenced organism</font> and you can also directly input the total sequence of that specific gene if you’ve already got the sequence.
 
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user can estimate the cost of primer synthesis.
 
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In the output, you can receive results of optimal primers for your gene and associated information of each candidate, this includes melting temperature, GC content, self annealing score etc.
 
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This Program provides an automatic <font color=dodger blue>ONE-STEP primer design service</font> of biobrick for iGEM communty to access all available <font color=dodger blue>genomic parts</font>.
 
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<center>[[File:SynthoPrime.jpg|700px|link=http://120.126.44.58/SynthoPrime/|caption]]</center>
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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.
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==<font size=5><font color=crimson>'''HOWTO: User Inputs'''</font></font>==
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HOWTO: <font color=red>User Inputs</font>  
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{|
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[[File:SynthoPrime manual p1.png|thumb|300px| '''STEP 1:''' Offer your sequence to be ‘biobricked’ by direct pasting your DNA or specifying by names of organism, replicon and gene.]]
[[File:SynthoPrime manual p1.png|thumb|300px| '''STEP 1:''' Offer your sequence to be ‘biobricked’ by direct pasting your DNA or specifying by names of organism, replicon and gene.]]
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[[File:SynthoPrime manual p2.png|thumb|300px| '''SETP 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.]]
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[[File:SynthoPrime manual p2.png|thumb|300px| '''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.]]
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HOWTO: <font color=red>Output Reading</font>  
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<center><html><object width="640" height="360"><param name="movie" value="http://www.youtube.com/v/6n_l3rCVS_g?version=3&amp;hl=zh_TW"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/6n_l3rCVS_g?version=3&amp;hl=zh_TW" type="application/x-shockwave-flash" width="640" height="360" allowscriptaccess="always" allowfullscreen="true"></embed></object></html></center>
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==<font size=5><font color=crimson>'''HOWTO: Output Reading'''</font></font>==
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References and Feedback
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<center><html><object width="640" height="480"><param name="movie" value="http://www.youtube.com/v/DTSXX2i7yjM?version=3&amp;hl=zh_TW"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/DTSXX2i7yjM?version=3&amp;hl=zh_TW" type="application/x-shockwave-flash" width="640" height="480" allowscriptaccess="always" allowfullscreen="true"></embed></object></html></center>
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==<font size=5><font color=crimson>'''References and Feedback '''</font></font>==
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[[File:SynthoPrime manual p7.png|thumb|630px| We would be more than happy to receive your comments and suggestions.]]
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[[File:SynthoPrime manual p7.png|thumb|630px| '''We would be more than happy to receive your comments and suggestions.''']]
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</center>

Latest revision as of 01:13, 29 October 2011

Slide Down Box Menu with jQuery and CSS3


Contents

Introduction

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


caption

[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.
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