Development and Application of a Software Tool/Package for Pan-Genomic Analysis

Continuing scientific progress in genetics allows us to better understand how structural variations in an organism’s gene content can lead to diversity within a species. By analyzing the sum of the genes for an entire species, we can construct a pangenome for the species. The pangenome of a species is the set of all genes present in all sub-species of a species. It consists of the core genome, which represents the genes present in all sub-species, and a variable genome, which refers to genes not present in all sub-species. micropan is an R package designed for the study of microbial pan-genomics. The genomes of prokaryotes (microbes) are relatively simple, leading to relatively simple construction of their pangenome. By comparison, plant genomes are highly repetitive and complex in comparison, and there is no general tool/package developed for pangenome construction for plant species. Due to the computational requirements of constructing such a pangenome, the tool/package required needs to be more flexible, efficient and robust than micropan. In this paper, we developed a pangenome construction pipeline that works for both prokaryotes and eukaryotes. The design of this pipeline will allow it to adapt to different selections of gene annotation and gene clustering methods. With a more efficient and robust tool/package constructed, future research can discover how to extend it from draft or finished genomes to sequencing reads.

• Publication year

  2019

• Venue

  IEEE Annual Information Technology, Electronics and Mobile Communication Conference

• Publication date

  2019-10-01

• Fields of study

  Biology, Computer Science

• Identifiers
  DOI 10.1109/IEMCON.2019.8936300
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

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