Validation issues can delay the processing of your submissions to GenBank. To avoid one type of delay, use the new “expected genome size” API to check the length of your genome assembly before submission.
The API compares the size of submitted genome assemblies to the expected genome size range for the species to identify outliers that can result from errors such as:
incorrect organism assignment
metagenome submitted as an organism genome
targeted sub-genome assembly not flagged as partial genome representation
gross contamination with other sequences
You can check in advance for these possible problems using the API. The API accepts the taxid for the species (taxid = Taxonomy ID – see our Taxonomy quick start guide on how to find the taxid for a given species) and the length of your assembly (excluding gaps and runs of Ns) as input and returns XML with the expected length, the acceptable range, and a status that tells you whether your assembly is too large, too small, or within the acceptable range. Look for <length_status>within_range</length_status> which confirms that your sequence passes the test!
We have released a new version of the Prokaryotic Genome Annotation Pipeline (PGAP), available on GitHub. The new release includes the ability to ignore pre-annotation validation errors (–ignore-all-errors). This new feature allows you to produce a preliminary annotation for a draft version of the genome, even one that contains vector and adapter sequences or that is outside of the size range for the species. This draft annotation should be helpful with your ongoing work on the genome assembly. Please keep in mind that these pre-annotations and assemblies with contaminants or other errors are not suitable for submission to GenBank.
Another new feature allows you to provide the name of the consortium that generated the assembly and annotation so that this information appears in the final GenBank records. For more details, consult our guidelines on input files.
See our previous post and our documentation for details on how to obtain and run PGAP yourself.
Next on our to-do list is a module for calculating Average Nucleotide Identity (ANI) to confirm the assembly’s taxonomic assignment. Stay tuned!
We have a new and improved search experience for viral genes from select human pathogens. When you search for a virus such as HIV-1 (more examples below), you now get an interactive graphical representation of the viral genome where you can see all the annotated viral proteins in context. Clicking on the gene / protein objects allows you to access sequences, publications, and analysis tools for the selected protein. This new feature is designed to help you quickly find information relevant to your research on clinically important viruses.Figure 1. Top: The virus genome graphic result for a search with HIV-1 with access to analysis tools, downloads, and relevant results in the Genome and Virus resources. Bottom: The result obtained by clicking the env gene graphic, which provides links to protein and nucleotide sequences, the literature, analysis tools, and downloads.
Try it out using the following example searches and let us know what you think!
How does it work? Download PGAP from GitHub, provide some basic information and the FASTA sequences for your genome sequence, and run the pipeline on your own machine, compute farm or the cloud. PGAP will produce annotation consistent with NCBI’s internal PGAP. Submit the resulting annotated genome to GenBank through the genome submission portal, and get an accession back.
As with any other submitted assembly, PGAP-annotated genomes will be screened for foreign contaminants and vector sequences at submission. Any annotated assemblies that don’t pass may need to be modified. We are developing an automated process to handle these edits!
We are also working on other improvements to stand-alone PGAP such as a module for calculating Average Nucleotide Identity (ANI) to confirm the assembly’s taxonomic assignment. Stay tuned for new developments!
If you are a consumer or producer of AGP (A Golden Path) files for genome assemblies, please read on. We’d like your feedback on the proposed changes described here.
As you know, AGP files are used to describe the structure of certain genome assemblies. The AGP file format has not kept up with changes in sequencing technology or International Sequence Database Collaboration (INSDC) feature usage. NCBI is therefore proposing to extend the current AGP v2.0 specification to add new linkage evidence types and a gap type of “contamination” as detailed below and described in the AGP v2.1 proposed specification.
NCBI announces Annotation Release 100 of the Pacific white shrimp (Penaeus vannamei) genome in RefSeq, based on the assembly (GCF_003789085.1) submitted by the Institute of Oceanology, Chinese Academy of Sciences. The Pacific white shrimp is one of the most important shrimp species in fisheries and aquaculture and represents the first decapod to have its genome annotated by NCBI. We predicted 24,987 protein coding genes with evidence from alignment of six billion RNA-Seq reads and homology with invertebrate proteins. This annotation will enable genomic research in this commercially important species.
If you’ve been searching in Gene, Nucleotide, Protein, Genome or Assembly databases, you’ve probably noticed the new search experience we introduced in September to interpret several common language searches and offer improved results. We’re excited to announce we’ve added as-you-type suggestions to the search bar in these databases.
Here’s a peek at the new menu in the NCBI Gene database.
Figure 1. Typing into the search box brings up automatic suggestions of the most popular queries.
Earlier this year, we announced the release of a new and improved search feature that interprets plain language to give better results for common searches. This feature, originally developed in NCBI Labs and later released on the NCBI All Databases search, is now available across several NCBI resources: Nucleotide, Protein, Gene, Genome, and Assembly. Whether you are searching for a specific gene or for a whole genome, you will now retrieve NCBI’s best results regardless of the database you search.
The image below shows the results for a search for human INS in the Nucleotide database. Even though this is a Nucleotide search, the results include relevant information from Gene, Protein, Taxonomy, plus links to the NCBI reference sequences (RefSeq) as well as access to BLAST and the insulin gene region in NCBI’s genome browser, the Genome Data Viewer.Figure 1. The new natural language search result in the Nucleotide database from a search for human INS.
Try out this new search capability and let us know what you think. And keep visiting the NCBI Labs search page to try our latest experiments, which we’ll also announce here on NCBI Insights.