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NCBI News, June 2010

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New Databases and Tools

Selected Structures

A new Selected Structures filter is available with Entrez Structure (MMDB) search results. This feature provides a way of sorting results into subsets based on characteristics of the retrieved records. Available subsets are keyed to protein domain families, source organisms, the presence of specific molecular complexes, and the presence of links to literature from PubMed or PubMed Central. The Selected Structures filter links appear in a box in the upper right corner of the Structure search result pages. Clicking on any of the linked numbers produces a subset of the results with the listed property. A portion of the results of a search for “p53 tumor suppressor” in the Structure database with the Selected Structures feature is shown below. Clicking on the filter for those records with protein-DNA complexes (green arrow) narrows the results to the four structures that have bound DNA (lower panel).

Selected_structures.png

See the structure help documentation to read more about Selected Structures.

New Nucleotide and Protein Pages

The Nucleotide and Protein pages have been updated with a new format and display settings. One important new feature is the ability to download coding sequence (CDS) regions as FASTA formatted sequences directly from the parent records. CDS downloads can be accessed using the new “Send” menu in the upper right of single or multiple record displays. See the note on the NCBI Facebook page for additional details.

Microbial Genomes

Twenty-one finished microbial genomes were released in June 2010. The original sequence data files submitted to GenBank/EMBL/DDBJ are available on the FTP site: ftp.ncbi.nih.gov/genbank/genomes/Bacteria/. The RefSeq provisional versions of these genomes are also available: ftp.ncbi.nih.gov/genomes/Bacteria/.

GenBank News

GenBank release 178.0 is available through the web and FTP sites. The current release includes information available as of June 11, 2010. The Release Notes provide more details: ftp.ncbi.nih.gov/genbank/gbrel.txt

Updates and Enhancements

Genome Workbench

Genome Workbench version 2.1.0 is available with numerous fixes and enhancements, giving researchers an even more powerful tool. Enhancements include an improved tree viewer used for phylogenetic tree analysis, integration of the MUSCLE alignment tool, and numerous updates to graphical views. Release notes for this version provide details on new features and bug fixes.

Genome Workbench is available for Windows, Linux, and Mac OS X and can be downloaded from the homepage: www.ncbi.nlm.nih.gov/projects/gbench/.

PubMed Central Turns Ten

PubMed Central celebrated its 10th Anniversary this year. Created as a free, online archive in 2000, it has grown to contain two million articles from 37,000 journals, over 600 of which are full deposit journals. A complete history has been compiled in the May-June issue of the NLM Technical Bulletin. NCBI celebrated the anniversary with a short symposium with speakers both from the NCBI and the outside community in May 2010.

PubMed

Recent improvements to PubMed include an updated Advanced Search page that provides a better-integrated and more intuitive mechanism for constructing complex searches and the ability to select what data are sent through the E-mail option on the Send menu. The improved Advanced Search page and changes to the E-mail option are described in more detail in articles e9 and e10 in the May-June 2010 issue of the NLM Technical Bulletin.

MyNCBI

My NCBI now allows sign-in by partner organization accounts. The improvement is described in more detail in the recent NLM Technical Bulletin.

YouTube

Four How-to Tutorial videos have been added to NCBI’s YouTube channel: www.youtube.com/ncbinlm. The following are the currently available instructional videos:

Announce Lists and RSS Feeds

Eighteen topic-specific mailing lists are available which provide email announcements about changes and updates to NCBI resources including dbGaP, BLAST, GenBank, and Sequin. The various lists are described on the Announcement List summary page: www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html. To receive updates on the NCBI News, please see: www.ncbi.nlm.nih.gov/About/news/announce_submit.html.

Twelve RSS feeds are now available from NCBI including news on PubMed, PubMed Central, NCBI Bookshelf, LinkOut, HomoloGene, UniGene, and NCBI Announce. Please see: www.ncbi.nlm.nih.gov/feed/.

Users can also stay updated on NCBI’s resources on Facebook (www.facebook.com/ncbi.nlm) and Twitter (twitter.com/NCBI).

Send comments and questions about NCBI resources to: vog.hin.mln.ibcn@ofni, or by calling 301-496-2475 between the hours of 8:30 a.m. and 5:30 p.m. EST, Monday through Friday.

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