Phylogenetic trees based on the NJ algorithm.

<p>Phylogenetic trees showing species evolution analysis for the 45 strains based on the NJ algorithm. The left graph is based on the gene distance matrix for core gene clusters, and the right graph is based on indel variations in core-gene clusters.</p

PanWeb: A web interface for pan-genomic analysis

<div><p>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 <a href="http://www.computationalbiology.ufpa.br/panweb" target="_blank">http://www.computationalbiology.ufpa.br/panweb</a>.</p></div

Name and description of each graph.

<p>Name and description of each graph.</p

Comparison of the original results of FGAP and after manual curation with GapBlaster.

<p>Comparison of the original results of FGAP and after manual curation with GapBlaster.</p

Gap closure results for GAGE Assemblies.

<p>Gap closure results for GAGE Assemblies.</p

Comparison of the features of GapBlaster, FGAP and GapFiller.

<p>Comparison of the features of GapBlaster, FGAP and GapFiller.</p

GapBlaster—A Graphical Gap Filler for Prokaryote Genomes

<div><p>The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at <a href="https://sourceforge.net/projects/gapblaster2015/" target="_blank">https://sourceforge.net/projects/gapblaster2015/</a>. It requires Sun JDK 8 and Blast or Mummer.</p></div

Sequencing information of the genomes used in the analysis.

<p>Sequencing information of the genomes used in the analysis.</p

Information of the reference genomes used to validate the filled-in gaps.

<p>Information of the reference genomes used to validate the filled-in gaps.</p

Gap closure results for the <i>Corynebacterium</i> genome.

<p>Gap closure results for the <i>Corynebacterium</i> genome.</p