Introduction

SoDpipe is an integration pipeline for automatically analyzing redundant gens and their regulation in prokaryotes. SoDpipe provides a framework to support genomic surveillance of the occurrence, gene expression and adaptive evolution from the perspective of gene redundancy for prokaryotes. SoDpipe takes both genome assembly and whole genome sequencing data as input and automatically performs the analysis of the data all through a single command-line instruction. It generates a detailed report of the duplicated gene clusters, types of translation initiation signals (SD-like, TA-like, Atypical, or no signal), signal motifs, and the start site of the signal. The pipeline is potentially extendable by adding new rules and will substantially reduce the efforts in sending commands.


Importance and Applications

  • Provides a framework to support genomic surveillance of the occurrence and expression of duplicated genes.

  • To gain understanding of the regulation of protein synthesis for prokaryotes.

  • To aid the study of the evolution of duplicated genes.

  • Suitable for all kinds of genomic data.

The process diagram for genome assembly data

Procedures and outputs:

The process diagram for whole genome sequencing data

Procedures and outputs:

References

  • Hu G-Q, Zheng X, Yang Y-F, Ortet P, She Z-S, Zhu H. ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Research 36, D114-D119 (2007).

  • Zheng X, Hu GQ, She ZS, Zhu H. Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes. BMC Genomics 12, 361 (2011).

  • Hu GQ, Zheng X, Zhu HQ, She ZS. Prediction of translation initiation site for microbial genomes with TriTISA. Bioinformatics 25, 123-125 (2009).

  • Koster J, Rahmann S. Snakemake-a scalable bioinformatics workflow engine. Bioinformatics 34, 3600 (2018).

    • Citation

  • Peihong Wang, Qian Guo, Longshu Yang, Mo Li, Chunhui Wang, Xiaoqing Jiang,Huaiqiu Zhu, Prokaryotic genome evolution: a moderate profusion of genetic elements.