Tochingyuet (Talk | contribs) |
Tochingyuet (Talk | contribs) |
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− | + | <center><h1> Instructions</h1></center> | |
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<h3>Create Your Account</h3> | <h3>Create Your Account</h3> | ||
<img src="https://static.igem.org/mediawiki/2017/d/de/CUHK_register.png" width="20%" height="auto" style="float: left"> | <img src="https://static.igem.org/mediawiki/2017/d/de/CUHK_register.png" width="20%" height="auto" style="float: left"> | ||
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<h3>Design your toehold switch</h3> | <h3>Design your toehold switch</h3> | ||
<br><p style="font-family: roboto;font-size:115%;"> | <br><p style="font-family: roboto;font-size:115%;"> | ||
− | Input target RNA sequence | + | <h4>Input target RNA sequence</h4> |
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User can input target RNA in plain text or FASTA file with numbers, space, newline, uppercase, lowercase, T or U. | User can input target RNA in plain text or FASTA file with numbers, space, newline, uppercase, lowercase, T or U. | ||
Target RNA sequences will be transformed to uppercased DNA sequence. All downstream process will use this format. Sequences less than 30 bp will be rejected. After procession of input, a page with all user inputs will prompt for user to check and confirm. Rejected sequences will also be shown. | Target RNA sequences will be transformed to uppercased DNA sequence. All downstream process will use this format. Sequences less than 30 bp will be rejected. After procession of input, a page with all user inputs will prompt for user to check and confirm. Rejected sequences will also be shown. | ||
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Start point will move to right for one nucleotide if the previous window sequence is rejected. Switch design process will continue if the window sequence passed the first examination. | Start point will move to right for one nucleotide if the previous window sequence is rejected. Switch design process will continue if the window sequence passed the first examination. | ||
<br> | <br> | ||
− | < | + | <h4>Input parameters:</h4> |
− | Input parameters: | + | |
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• Choose your cloning method (optional) | • Choose your cloning method (optional) | ||
<br> | <br> | ||
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RFC standard check are specifically added for iGEMers. The program can help you to eliminate switches with illegal sites. | RFC standard check are specifically added for iGEMers. The program can help you to eliminate switches with illegal sites. | ||
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− | < | + | <h4>Output option </h4> |
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− | Output option | + | |
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• Counting rare codon | • Counting rare codon | ||
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After all target RNA sequences are processed, BLASTn will be done for every legal window sequences if user ticked this option. BLASTn result will be saved in txt file with switch number as file name. | After all target RNA sequences are processed, BLASTn will be done for every legal window sequences if user ticked this option. BLASTn result will be saved in txt file with switch number as file name. | ||
<br> | <br> | ||
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Revision as of 12:10, 29 October 2017