On Wednesday, February 14, 2018, NCBI will present a webinar that will show you how to quickly retrieve sequences in any format from NCBI.
Date & time: Wed, Feb 14, 2018 12:00 PM – 12:30 PM EST
Ever need to quickly grab a protein or nucleotide sequence in FASTA or another format from NCBI? This NCBI Minute will show you how to accomplish this using the nucleotide and protein web pages, an NCBI URL, and – the most flexible way – through the commandline EDirect client that accesses the E-Utilities API.
After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.
Need a refresher of what NCBI offers? Or just feel you aren’t taking full advantage of NCBI resources? Check out some of NCBI’s most recent recordings of NCBI Minute webinars up on the NCBI YouTube channel.
On Tuesday, November 28, 2017, NCBI will present an update to the webinar originally presented on November 8, 2017 about the new API keys. In this updated webinar, you will learn about the relationships between API keys, NCBI accounts and IP addresses and see additional details about rates of access and server messages. You will also get answers to many important questions asked in the original webinar.
Date and time: Wednesday, November 8, 2017 12:00-12:30PM EST
After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.
The newest video on the NCBI YouTube channel introduces the Sequence Viewer embedding API. A few quick examples illustrate how easy it is to embed Sequence Viewer into your own pages.
Sequence Viewer is a graphical view of sequences and color-coded annotations on regions of sequences stored in the Nucleotide and Protein databases.
Subscribe to the NCBI YouTube channel to receive alerts about new videos ranging from quick tips to full webinar presentations.
This blog post is intended for geneticists and dataflow engineers who need to compare genetic variants.
Have you ever tried to determine if two genetic variants are the same? If so, you’re not alone. There are competing ways to represent variants, handling ambiguous assignments, as well as reconciling updates to underlying sequence models. To help you with these problems, we’re introducing a new set of web services for comparing and grouping variants.
NCBI has scheduled the next round of HTTPS tests, following up from the initial tests performed on September 15.
The schedule for these tests is as follows (all times are EDT):
NCBI offers extensive collections of sequences through its BLAST services (http://blast.ncbi.nlm.nih.gov) for comparing and identifying DNA, RNA and protein sequences. NCBI now deposits descriptions of these sequence collections, known as BLAST databases, in a special database called blastdbinfo that you can access through the Entrez Programming Utilities (E-Utilities). Using blastdbinfo, you can enable a program to find an appropriate database and then send BLAST searches to that database using either the BLAST URL API or standalone BLAST (installed locally).
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.