This program was written by Luca Comai and Tyson Howell. The program queries the user in the shell window for search parameters (barcode length, number, minimum genetic distance between barcodes, cycles of random attempts, and GC content). Depending on the chosen parameters, the few last possible barcodes of a type might be rare among all the possible random choices. if this happens, the program gets stuck trying to randomly generate highly improbable barcodes. The program starts with a seed barcode and it compares each new random product to the accepted barcodes. Once the set number of barcodes (or attempts) has been reached, the program joins the barcodes to the sequences of the Illumina paired end adapters and prints them to a file.
If you rather get tested barcodes right away, we have a list of 96 functional barcodes available here. This list includes both the barcodes and the complete oligonucleotides to be ordered. For more background information on barcodes, check out our instructional videos here.
To get Barcode Generator click on the Download link. Version 2.8 was written and tested for Python 2.5 to 2.6. Its function is exemplified by the output shown below.
__________________________________________INPUT and OUTPUT Example (IDLE shell window) BARCODE GENERATOR by LC and TH --***--- Plant Biology and Genome Center UC Davis This program generates barcodes of a desired length, distance, and GC content The primer sequences currently used are the illumina paired end primers Enter LENGTH as an integer (i.e. 4) Barcode length: 5 Enter the number of barcodes (default is LENGTH x 5) Total number of barcodes: 96 Enter the minimum number of different bases between barcodes (default is LENGTH/2, i.e. 7->3, 4->2) Min. no. of different bases between barcodes: 2 Enter desired GC content range in percentages (i.e. 50 ->50%) Minimum GC content (default is 0):20 Maximum GC content (default is 100):80 The default number of random codes to test is 10000. Do not enter more than a million How many attempts?:100000 RESULTS good barcodes and GC content: ['a', 'a', 'a', 'c', 'c'] 40 % ['a', 'a', 'c', 'a', 'g'] 40 % ['a', 'a', 'g', 'c', 'g'] 60 % [etc. etc.] ['t', 't', 't', 'g', 't'] 20 % number of tested barcodes: 284 number of good barcodes: 96 base compositions by position ['a', 'c', 't', 'g'] [20, 27, 26, 23] ['a', 'c', 't', 'g'] [25, 24, 23, 24] ['a', 'c', 't', 'g'] [25, 22, 24, 25] ['a', 'c', 't', 'g'] [21, 28, 24, 23] ['a', 'c', 't', 'g'] [25, 22, 23, 26] A file called barcode.txt has been generated. It contains the adapter sequences with each barcode in lower case >>> ___________________________________________ end of shell window A text file is generated and looks like this: These are the barcodes of length 5 with a distance of 2 bases >adA2_aaccg aaccgAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG >adB2_aaccg ACACTCTTTCCCTACACGACGCTCTTCCGATCTcggttT etc. ___________________________________________ end of file example
The research experience on which the Python pages are based is funded by the National Science Foundation Plant Genome grant DBI-0733857 (Functional Genomics of Polyploids), NSF Plant Genome award DBI-0822383, TRPGR: Efficient identification of induced mutations in crop species by ultra-high-throughput DNA sequencing, and National Institutes of Health R01 GM076103-01A1 (Dosage dependent regulation in hybridization) to LC.
To get Barcode Generator click on the Download link. Version 2.8 was written and tested for Python 2.5.2
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