Optiseed mRNA vaccine design
Introduction
5'cap
5'UTR
Orf
3'UTR
Poly(a)




    COMPRASION























Paste or type your ORF here:

The following parameters are
all necessary for mRNA design

a: a: Evaluation formula selection.1,2,3 is allowed.

k: >k: The larger the number of seeds, the higher the number of steps per mutation.<

     steps: Steps are the number of inner loops, and the longer the sequence and the larger k, the larger the steps must be.

out: Out:The number of outer loops, which determines how many initialization ranges from 1 to 30.

eva-lambda: 0 1 2 3 4 5 Eva lambda:evaluate the hyperparameters that balance MFE and CAI in Formula 1. The larger the lambda, the higher the CAI weight. When lambda=0, only MFE is optimized.
evax: 1 2 Eva lambda:evaluate the hyperparameters that balance MFE and CAI in Formula 1. The larger the lambda, the higher the CAI weight. When lambda=0, only MFE is optimized.

sa_outer: Sa_outer, after how many cycles to enter annealing, it is recommended to use steps/2- steps/1.

sa_inner: Sa_inner: The number of operations performed each time annealing is entered. It is recommended that steps/5-steps/2.

m: m :be set to 1 by default, and the last few results should be displayed, which must be less than k

submit: 

Select optimization algorithm    

Random Forest MLP

UTR length:        

3'UTR

Natural utr with highly expressed genes                                    
Common proteins in the human body carry UTR, which is generally more stable


UTR that have been optimized



5'cap








Poly(a)


        
EGFP-38 means 38 such sequences, followed by the corresponding base of the option

         

Your results of ORF are here, and input the results into the add Molecule below to observe your ORF secondary structure(order:sequence,structures,mfe,cai,ga-ratio)

Other parts(The order is 5 'cap, 5' cap,3 'utr ,poly(a) ):



Welcome to Optiseed mRNA vaccine design!

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For first-time users of this optimization platform, this manual provides a detailed user guide.

Follow the steps in this manual to obtain the results you want.

Option 1: This is the ORF optimization part, which is achieved by using the FASTA format. Enter the ORF sequence (currently only uppercase letters are supported). Select the corresponding parameter on the right side (click the question mark to understand its specific meaning), then click Submit. After the progress bar disappears, your optimization results will be displayed.

Option 2: This section is optional. If you only want to optimize your ORF, you may skip this part. Option 2 is divided into four sections: 5'UTR, 3'UTR, 5'Cap, and Poly(A). Select the desired components, and the results will be generated in the result box after clicking on Structure.

The remaining part of the website is a comparison between existing sequences and linear designs, showcasing the advantages of our current algorithm. These modules do not affect the optimization process of your sequence.

If you have understood the design process of this platform, click the Leave button below and start your mRNA design!