PanWeb: A web interface for pan-genomic analysis

Abstract

With increased production of genomic data since the advent of next-generation sequencing (NGS), there has been a need to develop new bioinformatics tools and areas, such as comparative genomics. In comparative genomics, the genetic material of an organism is directly compared to that of another organism to better understand biological species. Moreover, the exponentially growing number of deposited prokaryote genomes has enabled the investigation of several genomic characteristics that are intrinsic to certain species. Thus, a new approach to comparative genomics, termed pan-genomics, was developed. In pan-genomics, various organisms of the same species or genus are compared. Currently, there are many tools that can perform pan-genomic analyses, such as PGAP (Pan-Genome Analysis Pipeline), Panseq (Pan-Genome Sequence Analysis Program) and PGAT (Prokaryotic Genome Analysis Tool). Among these software tools, PGAP was developed in the Perl scripting language and its reliance on UNIX platform terminals and its requirement for an extensive parameterized command line can become a problem for users without previous computational knowledge. Thus, the aim of this study was to develop a web application, known as PanWeb, that serves as a graphical interface for PGAP. In addition, using the output files of the PGAP pipeline, the application generates graphics using custom-developed scripts in the R programming language. PanWeb is freely available at http://www. computationalbiology.ufpa.br/panweb.

Comparative genomics study of Lactobacillus plantarum strains provides perspectives about proteins involved in the probiogenomics

“…It is possible to infer whether the pan-genome is opened or closed through the Heap Law (n = k.N-α), where n is the expected number of genes from the pan-genome or core genome for a given number of N samples; k and α are values calculated according to the adjustment curve, which can be performed for the mean and median of each distribution. If the value of the element α ≤ 1 implies that the pan-genome is opened, but if α> 1 the pan-genome is closed[27,51]. In this study, the value of α for 41 strains of L. plantarum is 0.6704 for the mean and 0.6697 for the median, implying that the pangenome of the species is open(Figure 1).…”

“…The PanWeb platform was adopted for pan-genomic analysis [27]. PanWeb is an online interface based on the Pan Genome Analysis Pipeline -PGAP, a script in Perl language, developed by Zhao and collaborators (2012) [28].…”

PGAP-X: extension on pan-genome analysis pipeline

“…However, it does not provide information about genome structure, gene distribution on the genome, and genetic variation. PanWeb serves as a web-based PGAP, and output results from PGAP will be presented as images by R scripts in panWeb [ 29 ]. PGAP did not integrate and interpret genome structure and gene distribution, which were also not included in panWeb consequently.…”

Pan4Draft: A Computational Tool to Improve the Accuracy of Pan-Genomic Analysis Using Draft Genomes

“…In both cases we compared the results of the pan-genomic analysis before and after the use of Pan4Draft. Pan-genomic analysis of the controls genomes and the genomes before the use of Pan4Draft was performed by PanWeb 21 and the pan-genomic analysis in Pan4Draft was performed by PGAP, as it was mentioned in earlier.…”