Optiseed mRNA vaccine design
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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' utr,3 'utr ,poly(a) ):

Welcome to Optiseed mRNA vaccine design!


          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 is the ORF optimization part, which is achieved by using the FAFTA format Enter the ORF sequence (currently only uppercase letters are supported). elect the corresponding parameter on the right side (for the parameter on the right, click the question mark to understand its specific meaning), click submit, and after the progress bar disappears, your optimization results will be obtained.
         Option 2 is an optional section. If you only want to optimize your ORF, simply skip this section. Option 2 is divided into four parts: 5'utr, 3'utr, 5'cap, and poly (a). Select their corresponding options, and your results will also
be generated in the box that appears after clicking on structure.
         The remaining part of the website is a comparison between existing sequences and linear designs, which will show you some of the advantages our algorithm currently has. Of course, these modules will not affect your sequence optimization.
         If you have understood the design process of this platform, click on the leave button below and start your mRNA design!



COMPRASION
index Standard value Current value estimate
CAI 0.6～1 0.621-0.663 normal
MFE indefinite -33.5 - -33.3 normal
GC indefinite 2 normal
TIME 0~4h 0 slower
Option1:
Your mRNA design will start from here, input your ORF sequence, check the relevant parameters, click submit, and then wait for the optimized mRNA sequence to be generated. If you only want to design ORF, just ignore Option2

Paste or type your ORF here:


The following parameters are all necessary for mRNA design,

a. k:
a: Evaluation formula selection.1,2,3 is allowed.
k: The larger the number of seeds, the higher the number of steps per mutation.

steps: out:
Steps are the number of inner loops, and the longer the sequence and the larger k, the larger the steps must be.
Out:The number of outer loops, which determines how many initialization ranges from 1 to 30.

eva-lambda: 0 1 2 3 4 5
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.
EvaX:evaluate the three parameters in Formula 2.

sa_outer: sa_inner:
m
Sa_outer, after how many cycles to enter annealing, it is recommended to use steps/2- steps/1.
Sa_inner: The number of operations performed each time annealing is entered. It is recommended that steps/5-steps/2.
m :be set to 1 by default, and the last few results should be displayed, which must be less than k

submit:





Option1:ORF
An open reading frame (ORF) is the normal nucleotide sequence of a structural gene.
Option2:5',3'UTR
The 5' and 3' UTRs flanking the coding region regulate mRNA translation, half-life and subcellular localization.
Option2:5'CAP
The 5'cap protects the mRNA sterically from degradation by exonucleases, and it works synergistically with the poly(A) tail at the 3' end,
Option2:poly
The Poly(a) protects the mRNA sterically from degradation by exonucleases, and it works synergistically with the poly(A) tail at the 3' end,
Option2: UTR
Option2:   5'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
Sequences targeting specific cell types



Result

  • click  to view the ORF results you obtained





introduction

A fast, effective, and flexible codon optimization tool.

Option2:   5'cap







Option2：  poly(a)


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