Unlike conventional bulk measurements, which only display the mean of data, ALiVE opens the door to vast gene reporter multiplexing and single-cell transcriptomics. We developed an end-user friendly app to compute a reporter's encoding potential: "Silentcode" is a software to calculate the possible combinations of silent mutations within a transcript of interest. During the development of ALiVE, our transcript of choice was a luciferase due to versatile applications, e.g. luminescence assays and qPCR. By using Silentcode, we were able to calculate the number of different markers we could create (2,24*10^272) without impacting the encoded protein itself. Silentcode's intuitive interface allows the user to enter the nucleotide sequence into the input field and retrieve the data after one click plus possible data volume in bytes. This could nowadays be applied for cell differentiation experiments or function as barcodes, but in the future also contribute as a synthetic-biology storage medium for technical data.
Workflow
- Enter your sequence
- Press Launch
- Read output
Output
>fluc
Sequence Name
sequence:GAAGATGCCAAGAACATCAAGAAGGGCCCTGCTCCTAGATACCCTCTGGAAGATGGAACCGCTGGCGAGCAGCTGCACAAGGCCATGAAGAGATACGCTCAGGTGCCCGGCACAATCGCCTTCACAGATGCCCACATCGAAGTGAACATCACCTACGCCGAGTACTTCGAGATGAGCGTGCGGCTGGCCGAAGCTATGAAGCGATACGGCCTGAACACCAACCACAGAATCGTCGTGTGCAGCGAGAACAGCCTCCAGTTCTTCATGCCTGTGCTGGGCGCTCTGTTCATCGGAGTGGCTGTGGCTCCTGCCAACGACATCTACAACGAGCGCGAGCTGCTGAACAGCATGAACATCAGCCAGCCTACCGTGGTGTTCGTGTCCAAGAAGGGACTGCAAAAGATCCTGAACGTGCAGAAGAAGCTGCCCATCATCCAGAAAATCATCATCATGGACAGCAAGACCGACTACCAGGGCTTCCAGAGCATGTATACCTTCGTGACCAGCCATCTGCCACCAGGCTTCAACGAGTACGACTTCAAGCCCGAGAGCTTCGACAGAGACAAGACAATCGCCCTGATCATGAACAGCAGCGGCTCTACCGGACTGCCTAAAGGCGTTGCCCTGCCTCACAGAACAGCTTGCGTCAGATTCAGCCACGCCAGAGATCCCATCTTCGGCAACCAGATCAAGCCTGACACCGCTATCCTGAGCGTGGTGCCTTTTCACCACGGCTTCGGCATGTTCACCACACTGGGCTACCTGATCTGCGGCTTCAGAGTGGTGCTGATGTATCGCTTTGAGGAAGAACTGTTCCTGCGGAGCCTCCAGGACTACAAGATCCAGTCTGCTCTGCTGGTGCCTACTCTGTTCAGCTTCTTTGCCAAGAGCACCCTGATCGATAAGTACGACCTGAGCAACCTGCACGAGATCGCCTCTGGCGGAGCCCCTCTGTCTAAAGAAGTGGGCGAAGCCGTCGCCAAGAGATTTCATCTGCCCGGCATCAGACAAGGCTACGGACTGACCGAGACAACCAGCGCCATCCTGATCACACCTGAGGGCGACGATAAGCCTGGCGCTGTGGGAAAAGTGGTGCCATTCTTCGAGGCTAAGGTGGTGGACCTGGACACCGGCAAAACACTGGGAGTGAATCAGAGGGGCGAGCTGTGTGTCAGAGGCCCTATGATCATGAGCGGCTACGTGAACAACCCCGAGGCCACCAACGCTCTGATCGACAAGGATGGCTGGCTGCACAGCGGCGACATTGCCTACTGGGACGAAGATGAGCACTTCTTCATCGTGGACAGACTGAAGTCCCTGATCAAGTACAAGGGCTACCAGGTGGCCCCTGCCGAGCTGGAATCTATCCTGCTCCAGCATCCTAACATCCGCGACGCTGGTGTTGCTGGCCTGCCTGACGATGATGCTGGCGAACTTCCTGCTGCCGTGGTGGTGCTGGAACACGGCAAGACCATGACCGAGAAAGAAATCGTGGACTACGTGGCCTCTCAAGTGACCACCGCCAAGAAACTGAGAGGCGGCGTGGTGTTTGTGGACGAGGTGCCAAAAGGCCTGACCGGCAAGCTGGACGCCAGAAAGATCAGAGAGATCCTCATCAAGGCCAAGAAAGGCGGCAAGATCGCTGTC
sequence
bases: 1647
Number of Bases in the sequence
triplets: 549
Number of triplets in the sequence
| AA | BP | Triplet (AA name) | codons | GC |
|---|---|---|---|---|
| 0 | 0 | GAA (Glu): | 2 | 0,56 |
| 1 | 3 | GAT (Asp): | 2 | 0,5 |
| 2 | 6 | GCC (Ala): | 4 | 0,33 |
| 3 | 9 | AAG (Lys): | 2 | 0,44 |
| 4 | 12 | AAC (Asn): | 2 | 0,44 |
| ... | ||||
| 547 | 1641 | GCT (Ala): | 4 | 0,58 |
| 548 | 1644 | GTC (Val): | 4 | 0,44 |
Number of codons for the amino acid at position [AA] defined by the triplet starting at position [BP] with the specified GC content in close proximity.
Possible combinations of silent mutations: 2.2351680288680503E272 = 2^904 of 2^3294
Storage capacity: 113.0 Byte of 411 Byte
Storage capacity: 113.0 Byte of 411 Byte
Possible combinations of silent mutations in relation to the potential number. In the second line, this is given in bytes.
