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NCBI News, October 2009

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New Databases and Tools

New NCBI Homepage

The newly designed NCBI Homepage is more streamlined with resources, tools, and services divided into organized groups. The “All Resources” link provides a list of all NCBI resources while the subject lists below provide resources according to those headings. The “How To” link goes to lists of short, FAQ-like questions and answers on many topics. There are also How To help links within each subject category. The default “All Databases” search in the Search box performs a global query search on all Entrez Databases. A featured resource article in the next NCBI News issue will describe the New Homepage in detail.

New PubMed Homepage and Search Service

The PubMed service has a new design and provides new functionality. The PubMed Redesign article in the NLM Technical Bulletin outlines changes and describes how to find previously used functionalities.

www.nlm.nih.gov/pubs/techbull/so09/so09_pm_redesign.html

A featured resource article in the next NCBI News issue will describe improvements and enhancements in detail.

Microbial Genomes

Twelve finished microbial genomes were added to the NCBI databases between September 14 and October 28. The original sequence data files submitted to GenBank/EMBL/DDBJ are 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 174.0 is now on the NCBI Web Service and FTP site. The current release incorporates sequence data as of October 16, 2009. Release notes with detailed information are on the FTP site: ftp.ncbi.nih.gov/genbank/gbrel.txt

Updates and Enhancements

PubMed Central

Two new pages have been added to the PMC site. The “New in PMC” page provides updates on PMC developments and features.

www.ncbi.nlm.nih.gov/pmc/about/new_in_pmc.html

The “Public Access and PMC” page provides information on the relationship between PMC and the NIH Public Access Policy.

www.ncbi.nlm.nih.gov/pmc/about/public-access-info.html

BLAST

BLAST version 2.2.22 is now available for download from the BLAST section of the NCBI FTP site.

ftp.ncbi.nih.gov/blast/executables/

BLAST 2.2.22 includes BLAST+ command-line applications. The BLAST News page provides an extensive list of improvements and BLAST+ application changes.

blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews#1

Publications

A new article summarizing Mammalian Gene Collection project will soon be published in Genome Research. The article is available electronically ahead of the print publication:

The MGC Project Team. “The completion of the Mammalian Gene Collection (MGC).” Genome Research. 2009 Oct 28 [Epub ahead of print]. PMID: 19767417.

Announce Lists and RSS Feeds

Three new mailing lists are available for updates and changes to NCBI resources: NCBI Structures, Conserved Domains, and BioSystems. Topic-specific mailing lists provide email announcements about changes and updates to NCBI resources including dbGaP, BLAST, GenBank, and Sequin. The Announcement List summary page describes the various lists and how to subscribe:

www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html.

The NCBI Announce mailing list sends notices on NCBI News updates and important announcements.

www.ncbi.nlm.nih.gov/About/news/announce_submit.html

Seven RSS feeds are now produced by NCBI including news on PubMed, PubMed Central, NCBI Bookshelf, LinkOut, HomoloGene, UniGene, and NCBI Announce.

www.ncbi.nlm.nih.gov/feed/

Comments and questions about NCBI resources may be sent to NCBI through electronic mail, 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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