Team:NYMU-Taipei/synthoprime

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== HOWTO: User Inputs ==
 
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==<font size=5><font color=crimson>'''Introduction'''</font></font>==
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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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<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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[[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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<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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[[File:SynthoPrime manual p5.png|thumb|630px|Main output page]]
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[[File:SynthoPrime manual p6.png|thumb|630px|Additional Info.]]
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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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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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