Team:NYMU-Taipei/synthoprime

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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.

By using [http://120.126.44.58/SynthoPrime/ SynthoPrime] program, you can design your own biobrick primers by selecting genes that you need with quantitative measures, including primer length, melting temperature and GC content. You can access any genes from sequenced organism and you can also directly input the total sequence of that specific gene if you’ve already got the sequence. user can estimate the cost of primer synthesis. 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. This Program provides an automatic ONE-STEP primer design service of biobrick for iGEM communty to access all available genomic parts.

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.	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.
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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-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.
+By using <font color=red>[http://120.126.44.58/SynthoPrime/ SynthoPrime]</font> program, you can <font color=medium blue>design your own biobrick primers</font> by <font color=medium blue>selecting genes</font> that you need with quantitative measures, including primer length, melting temperature and GC content.
-<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.
+<font color=medium 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.
 user can estimate the cost of primer synthesis.
 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.
-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>.
+This Program provides an automatic <font color=medium blue>ONE-STEP primer design service</font> of biobrick for iGEM communty to access all available <font color=medium blue>genomic parts</font>.
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