As you may know, we have been offering a new BLAST results (Figure 1) as a test page since April. In response to your positive reception and after incorporating many improvements that you suggested, we made the new results the default today, August 1, 2019.
You will still be able to access to the traditional results for a several months. This will provide you additional time if you need it to adjust your workflows or teaching materials to the new display.
BLAST is a powerful search tool, but often a search is just the beginning of the journey. We put ourselves in the shoes of a researcher who has just sequenced a handful of samples from the latest viral outbreak and tried to understand what information would be most useful. We also reached out to researchers in the field and asked: a) what questions do they really want to answer? and b) how can NCBI best provide the answers? Based on insights from those questions and answers, we developed the new Virus Sequence Search Interface (Fig. 1). The Search Interface is an NCBI Labs project, which means it is an experimental project, and we may modify the resource based on your feedback and experiences.
Figure 1. The Virus Sequence Selection Interface. The Virus Sequence Selection Interface accepts as input nucleotide and protein accessions, as well as FASTA and plain-text formatted sequences. The user selects either “Nucleotide” or “Protein,” depending on the sequence type, and selects the virus type from the pull-down menu below the text entry field.
NCBI will discontinue both the NCBI Genomes (chromosome) and the Human ALU repeat elements (alu_repeats) BLAST databases in October 2017.
Better alternatives to NCBI Genomes (chromosome)
The existing NCBI Genomes (chromosome) database does not offer complete and non-redundant coverage of genome data. The newly added NCBI RefSeq Genomes Database (refseq_genomes) and the RefSeq Representative Genomes Database (refseq_representative_genomes) are more useful alternatives to the chromosome database. You can select these databases from the database pull-down list on any general BLAST form that searches a nucleotide database (blastn, tblastn).
Figure 1. The nucleotide-nucleotide BLAST database menu with the recommended (RefSeq Genome and Representative genomes) and deprecated (NCBI genomes (chromosomes) and Human ALU repeats) databases highlighted.
This article is intended for GenBank data submitters with a basic knowledge of BLAST who submit sequence data from protein-coding genes.
One of the most common problems when submitting DNA or RNA sequence data from protein-coding genes to GenBank is failing to add information about the coding region (often abbreviated as CDS) or incorrectly defining the CDS. Incomplete or incorrect CDS information will prevent you from having accession numbers assigned to your submission data set, but there is a procedure that will help you troubleshoot any problems with the CDS feature annotation: doing a BLAST analysis with your sequences before you submit your data.
NOTE: We have changed BLAST search results displays since publishing this blog. For updated guidance on using Nucleotide BLAST (blastn) to help you troubleshoot coding region annotation, see the articles in the NCBI Support Center.
Here’s how to use nucleotide BLAST (blastn) and the formatting options menu to analyze, interpret and troubleshoot your submissions:
1. To start the BLAST analysis, go to the BLAST homepage and select “nucleotide blast”.
