MODEST allows the rapid and effective design of optimal MAGE oligos based on simple input, to achieve any mutation possible with MAGE. Simply input the desired modifications to receive optimized MAGE oligos that will create the modifications along with MASC primer sequences for validation. A manuscript for the software is being prepared.
Oligos created with MODEST is optimal for use with MAGE and recombineering methods where the methyl-directed mismatch repair (MMR) system is unfunctional. Please see online documentation for further details.
To get help, browse the online documentation. To report errors or ideas, please use the icon in the top right of the screen.
Choose a name for your project:
NC_000913.3-E_coli_K12_MG1655 NC_003197.1-Salmonella_typhimurium_LT2 NC_004567.2-Lactobacillus_plantarum_WCFS1 NC_004578.1-Pseudomonas_syringae_pv._tomato_str._DC3000 NC_010609.1-Lactobacillus_reuteri_JCM_1112 NC_017531.1-Pantoea_ananatis_AJ13355 Other..
You can upload your own GenBank file or choose from GenBank:
GenBank identifier [eg. NC_000913]:
Custom annotated GenBank file:
Please provide origin of replication (oriC) and termination region:
oriC/Origin of replication (positon or range)
Termination of replication (position or range)
See the documentation on creating your own genome configuration. If you have a genome config from a previous run, you can upload that instead of oriC/ter:
Custom genome configuration file:
Perform point mutations, insertions, deletions, translational knockouts and expression level modifications. See how in the instructions.
Load test data set (warning: overrides current data)
Download your text file: The file will NOT be stored on the server for later retrieval:
Upload a file (.txt)
Expand/Contract options
Oligo length (bp):
Minimum end homology (bp):
Long-insertion end homology (bp):
Select to enable 2° structure optimization: (Uncheck this box to force MODEST to center the mutation in all oligos)
2° structure optimization threshold (kcal/mol):
Upload or paste a barcoding library. Only needed if barcodes are specified in DNA modifications file. See documentation on barcoding libraries.
Upload barcoding library
# Barcoding Library file # Reference: Kosuri, S. et al. Scalable gene synthesis by selective amplification # of DNA pools from high-fidelity microchips. Nat. Biotechnol. 28, 1295-9 (2010). # PMID: 21113165 # DOI: 10.1038/nbt.1716 >PRIMERS F1 GTCGAGTTGATCCATGGTCT F2 TAGCGTGCGATAGATCCTCT F3 CCTTGAATCGACACTGCAGT F4 ACTTCCACGTTACCTAGGCT F5 CCATTCCACGTTCCAAGAGT F6 CAGTAACAAGGCAACCGAGT F7 GCAAGTAACCTGTAACGGCT F8 AGTCATAATCAACTCCGCGT F9 AGTCGAATATCCACCACCGT F10 ACTAACAACCGCCTTATCGT F11 GGCCGTATACCAGCTTAAGT F12 CTTAAGCACCACTCCTCGAT F13 AGCCTACCTCATCTGCGAAT F14 TATCACTTGGCCTCCTTCCT F15 ACTTACTGTCAGGTCGTCGT F16 AAGCAAGATTCTCGTCGGAT F17 TCTAATCTAGCGCGACGTCT F18 TTAGGTCGGCAGGTCAGTAT F19 AACACGTCCGTCCTAGAACT F20 AGTGTTGAGCGTAACCAAGT R1 TGACACAGACGCATAGGATC R2 GGCTCCTTGTTAGACCGATC R3 CGAACTCGCCAAGGTAGATC R4 GGATACTCACTGCTGCGATC R5 TCGGTACTAGGCTCCTGATC R6 CCACGCAAGGAGTTAGGATC R7 CATGAGTCTACGCCGTGATC R8 GACCTGTGCAATGTTCGATC R9 GCTTGGAGTAGCGTTCGATC R10 ACTAGCAGCTGACCTTGATC R11 GTTCTAGACTGGCTCGGATC R12 CCAGTCGGTAGTCAAGGATC R13 AGAGCCTCAGGTAACCGATC R14 ATGCGCGTTCCTTCTAGATC R15 GGTACCGTGTTGTTCCGATC R16 TGTAAGGCACATCTCGGATC R17 CCACAAGAGGCGCTATGATC R18 GGTTCCTTCGGAGTGTGATC R19 GCAAGCGGTACACTCAGATC R20 CAGGAGTTGTCTAGGCGATC >LIBRARY ID01 F1 R1 ID02 F2 R2 ID03 F3 R3 ID04 F4 R4 ID05 F5 R5 ID06 F6 R6 ID07 F7 R7 ID08 F8 R8 ID09 F9 R9 ID10 F10 R10 ID11 F11 R11 ID12 F12 R12 ID13 F13 R13 ID14 F14 R14 ID15 F15 R15 ID16 F16 R16 ID17 F17 R17 ID18 F18 R18 ID19 F19 R19 ID20 F20 R20