Overview Of Webserver
mRNAviewer aims for integrated optimization of mRNA sequence (including 5′ untranslated region (UTR), open reading frame (ORF) codon, and 3′ UTR) to improve gene translation in various biomedical applications. Users input the amino acid sequence of target protein and then choose the location where the mRNA is expected to be translated (human tissue type). mRNAviewer also provides several important features (e.g. secondary structure, miRNA binding sites, and RNA binding protein binding sites) of optimized sequence.
Web Interface And Analysis Results
mRNAviewer input
Users input the amino acid sequence of target protein. Next, users can choose tissue type (e.g. lymph node, spleen, and lung) depending on their applications. If users don't specify tissue type, the optimization will be run as general model.
mRNAviewer analysis result
mRNAviewer generates optimized sequence including 5′ UTR, ORF codon, and 3′ UTR. The start and end nucleotide position of each region are noted, and each region is marked with a different color. Notably, the Kozak sequence "GCCACC" is added before start codon "ATG" to facilitate translation initiation. Meanwhile, two tandem stop codons are added at the end of ORF to avoid the rea-through of translation. Along with the optimized sequence, mRNAviewer also provides several important features of mRNA. With a user-friendly interface, users can drag the lines or specify start/end positions to view these features in the region of interest. First, mRNAviewer provides the absolute count and percentage of each nucleotide. Next, mRNAviewer provides the secondary structure and minimum free energy (MFE) by integrating RNAfold webserver. Third, mRNAviewer provides miRNA binding sites by integrating miRBase. miRNA function posttranscriptionally by base-pairing to the mRNA 5′ UTR and 3′ UTR to regulate protein synthesis. The links in results can link users to the detailed miRNA information. Fourth, mRNAviewer provides the RNA binding protein (RBP) binding sites in by integrating RBPDB database. RBP have well-established roles in regulating mRNA translation efficiency and stability. By clicking the links in results, users can access to details of RBP.