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.
NCBI is retiring the e-PCR tool effective immediately. The good news is that an existing tool, Primer-BLAST, fills in nicely for the functions of both Forward and Reverse e-PCR, and has the additional benefit of de novo primer design.
A common task facing geneticists is to assay for sequence changes at particular locations in genes. These assays are often looking for changes in the coding exon of genes, and the target sequences are typically amplified using PCR from genomic DNA using a pair of specific primers. In this article, we will show you how to use NCBI Reference Sequences and Primer-BLAST, NCBI’s primer designer and specificity checker, to design a pair of primers that will amplify a single exon (exon 15) of the human breast cancer 1 (BRCA1) gene.
Here are the steps to follow to design primers to amplify exon 15 from human BRCA1: