RoDTIS: Robust DNA Targeting in silico

A script that returns the gene sequences of interest in an electronic PCR-like manner.

This script was used in Nielsen et al. (2018). Working title: Association of Outer Membrane Protein A.

Assumptions

• Python 3 is installed on machine.
• Biopython is installed on machine.
• User has bash terminal.
• The title of sequences are presumed to be in an NCBI-like format. For example, for assembly GCA_012732875.1_PDT000148291.2_genomic.fna, the contig identified as >AATDWI010000001.1 Escherichia coli strain 197080 SAMN05750861-rid6247213.denovo.001, whole genome shotgun sequence will be named as as the [gene]_AATDWI010000001.1 in the output. Without a space, the sequences may be interpreted as sequence names.

Input

Standard:

1. Create an Excel sheet with the gene name, primers, and size range of product as follows: E.g.:

2. RoDTIS.py Panel1.xlsx fasta_files/* > Output.fasta

Advanced:

RoDTIS allows for variable matching of the last half of the primer used, which sets it apart for simply matching the primer in the sequence.

• To use the advanced option, use the -s flag.
  • The -s flag must be used with an interval between 0.0-1.0.
    • The higher the number:
    • The lower the number:
  • e. g. RoDTIS.py -s 0.2 Panel1.xlsx fasta_files/* > Output.fasta

Output

Open FASTA file in the program of your choice, and view the genes within each fasta file.