DNA / RNA Sequence Pool Generator
poolgen is a general purpose Python module which generates different types of DNA and RNA sequences. The code is available as an open source repository on Bitbucket under a MIT Licence.
The following types of DNA or RNA sequences can be generated:
DeBruijn sequences
Random sequences
Sequences taken from randomly selected regions of longer biological vector sequences (like plasmids, phages etc.)
The program outputs a CSV file of generated sequences, like this:
10 DeBruijn sequences of DNA of length 20 nt [python3 generate.py 10 dbsdna 20 go.txt]
dbsACGT_k=3_0,TGCCCTAATCAGTTGGGTAC
dbsACGT_k=3_1,ACGTCGAAACCGCAAGCGGA
dbsACGT_k=3_2,TAGACTTTCTGAGGCTCCAT
dbsACGT_k=3_3,AGGCCTAGTCTTTGGAGACT
dbsACGT_k=3_4,GATTCACCCAATCGCTCCGT
dbsACGT_k=3_5,ACATATGTGCGGGTTAAACG
dbsACGT_k=3_6,ATTGGCGGGTTCGTCCTTTA
dbsACGT_k=3_7,TGAACTCTAGAGGATAAGTA
dbsACGT_k=3_8,CAAATCACCCGACGCCAGCT
dbsACGT_k=3_9,ATGTGACCCGGAAATTTGCC
If desired, poolgen can additionally verify if a generated DNA sequence is likely to have problems with PCR amplification, and only output those sequences which pass a PCR Primer Check.
The PCR Primer Check script itself can also be used to output all potential forward and reverse primers for a given DNA sequence.
A main application for poolgen is with the DNA origami scaffold selector, where it is applied to generate a pool of potential DNA scaffold sequences for a nanostructure.
See the Installation page to get started and then Generate Sequences.