As we described in an earlier post, GenBank uses average nucleotide identity (ANI) analysis to find and correct misidentified prokaryotic genome assemblies. You can now access ANI data for the more than 600,000 GenBank bacterial and archaeal genome assemblies through a downloadable report (ANI_report_prokaryotes.txt) available from the genomes/ASSEMBLY_REPORTS area of the FTP site. The README describes the contents of the report in detail. You can use the ANI data to evaluate the taxonomic identity of genome assemblies of interest for yourself.
The new ANI_report_prokaryotes.txt replaces the older ANI_report_bacteria.txt in the same directory. We are no longer updating the ANI_report_bacteria.txt file and will remove it after 31st May 2020.
A new version of the Prokaryotic Genome Annotation Pipeline (PGAP) is now available on GitHub. This release uses a new and improved version of tRNAscan (tRNAscan-SE:2.0.4) and includes our most up-to-date Hidden Markov Model and BlastRule collections for naming proteins.
Remember that you can submit the results of PGAP to GenBank. Or, if you are still improving the assembly and your genome doesn’t pass the pre-annotation validation, you can use the –ignore-all-errors mode to get a preliminary annotation.
RefSeq release 93 is accessible online, via FTP and through NCBI’s Entrez programming utilities, E-utilities.
This full release incorporates genomic, transcript, and protein data available as of March 13, 2019. It contains 192,722,653 records, including 135,670,032 proteins, 25,840,272 RNAs, and sequences from 88,816 organisms.
We now have many improvements to our search functionality on NCBI’s global search page that will benefit users trying to find prokaryotic assemblies and genes. These improvements aim to highlight the best results and provide links to related NCBI content, so you don’t have to sift through pages of results and navigate between different NCBI resources.
Given the size of modern sequence databases, finding the complete genome sequence for a bacterium among the many other partial sequences can be a challenge. In addition, if you want to download sequences for many bacterial species, an automated solution might be preferable.
In this post we’ll discuss how to download bacterial genomes programmatically for a list of species using the E-utilities, the application programming interface (API) to NCBI’s Entrez system of databases. We’ll also take advantage of NCBI’s redesigned Genome database, which links all genome sequences for a given species to one record, making it easy to obtain the desired sequences once you find the right Genome record. In principle you can apply the procedure below to other simple genomes that are represented by a single sequence. Future posts will address additional considerations that apply to complex, eukaryotic genomes.