Category Archives: Entrez
Updated and improved collection of RefSeq representative genome assemblies now available
We have updated the collection of representative genome assemblies for Bacteria and Archaea. As announced in April, this set is now recalculated three times a year. We selected a total of 11,727 prokaryotic assemblies to represent their respective species among the 192,000 assemblies in RefSeq. Six hundred and thirty-five species were included in the collection … Continue reading Updated and improved collection of RefSeq representative genome assemblies now available
Improved Search Now Available Across NCBI Databases
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 … Continue reading
Posted by in assembly, Entrez, Gene, Genome, Genome Browser, NCBI Labs, nucleotide, Protein, What's New
Upcoming Changes to EST and GSS Databases
As of December 1, 2018, all records from the databases for Expressed Sequence Tags (EST) and Genome Survey Sequences (GSS) will reside in NCBI’s Nucleotide database. This change will provide a single point of access for all GenBank sequence data … Continue reading
Posted by in BLAST, e-utilities, Entrez, NCBI Nucleotide, Submissions, What's New
Test drive a new sequence search experience at NCBI Labs
We know it’s not always easy to find the sequence data you’re after at NCBI. Maybe it’s because you’re no expert at constructing queries, and you end up with no results or too many results. Or maybe you’re an Entrez wizard, … Continue reading
Posted by in Entrez, genome assemblies, NCBI Labs, sequences, What's New
5 NCBI articles in 2018 Nucleic Acids Research database issue
The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on … Continue reading
GenBank release 223.0 is available via FTP, Entrez and BLAST
GenBank release 223.0 (12/15/2017) has 206,293,625 traditional records (including non-bulk-oriented TSA) containing 249,722,163,594 base pairs of sequence data. In addition, there are 551,063,065 WGS records containing 2,466,098,053,327 base pairs of sequence data, 201,559,502 TSA records containing 181,394,660,188 base pairs of … Continue reading
Posted by in BLAST, Entrez, Genbank, What's New
GenBank release 221.0 is available via FTP, Entrez and BLAST
GenBank release 221.0 (8/13/2017) has 203,180,606 traditional records containing 240,343,378,258 base pairs of sequence data. In addition, there are 499,965,722 WGS records containing 2,242,294,609,510 base pairs of sequence data, 186,777,106 TSA records containing 167,045,663,417 base pairs of sequence data, and … Continue reading 
Posted by in BLAST, Entrez, Genbank, What's New
Exploring Entrez Direct: Parsing the XML Output of E-utilities
Entrez Direct is a UNIX/LINUX command-line interface to E-utilities, the API to the NCBI Entrez system. One of Entrez Direct’s most useful features is its ability to parse and reformat complex XML data returns from EFetch. In this post, we … Continue reading 
Posted by in Entrez, Entrez Direct, Quick Tips
The Second Offering of “A Librarian’s Guide to NCBI” at NIH
NCBI, in collaboration with NLM and the National Network of Libraries of Medicine NLM Training Center (NTC) at the University of Utah, recently presented the second offering of A Librarian’s Guide to NCBI. Health Sciences Librarians from 17 universities and … Continue reading 
Posted by in BLAST, Entrez, geo, National Library of Medicine, NCBI Education, training, What's New