Genome Upgrading

 

To improve the quality of draft genomes, some techniques are used to enhance their assembly. The Sanger capillary electrophoresis method, short-read sequence data, and whole genome assembly techniques are some examples. Even the most highly assembled draft genomes will have gaps, as sequencing biases make some regions difficult to assemble. In addition, genomes may contain regions with genomic polymorphism or repetitive genomic features.

Using a new technique called PBJelly, scientists can quickly and easily upgrade their sequences. This technique requires fasta format sequences and can improve de novo assemblies. Furthermore, it requires little or no annotation work for model organism communities. In contrast, a simple re-assembly can only upgrade low-quality regions and will lose existing annotations. However, Genome Upgrading preserves the majority of the assembled sequence.

With its new fast front-end server, PHASTER can process a typical bacterial genome in 1.5 minutes. Moreover, it has implemented several optimizations, including automatic algorithms that reduce the size of PHASTER's database and handle increased user traffic. This new tool can lookup over fourteen thousand previously annotated genomes and can produce a complete phage annotation in less than a minute. PHASTER also has a new user interface.

JCVI has a number of tools and services. For example, it offers BLAST services that allow users to search against genomes and proteomes. In addition, genome browsers allow interactive navigation of the genome, such as the JBrowse and GBrowse programs. Moreover, gene information pages can include functional search, domain structures, and literature relating to genes. Additionally, Textpresso allows users to access relevant literature.