NCBI News, March 2009 Print
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Saturday, 14 March 2009 19:21

NCBI News, March 2009

Peter Cooper, Ph.D.
NCBI
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Dawn Lipshultz, M.S.
NCBI
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Created February 12, 2009.

Featured Resource: The New Entrez Sequence View has an Emphasis on Discovery

NCBI now has an updated sequence view for nucleotide and protein records that provides better display options, links to analysis tools, and an emphasis on the discovery of related information in other NCBI databases (Figure 1). The new view retains the standard format of the sequence but has more obvious links to display FASTA, other formats, and specific subregions and features. The right-hand discovery column features direct links to analysis tools, and, most importantly, explicit links to valuable related information such as better-annotated sequences, and more information-rich databases such as Gene, HomoloGene, and PubMed. 

The format row at the top of the new view has direct links to display the sequence in FASTA format and to display the record and features in the NCBI Graphical Viewer (NCBI News, Aug 2008). Other less specialized reports such as ASN.1 and XML are available through the separate “More formats” list. A “Download” link to save the records in various formats to a local file and a “Save” link to store the records in the NCBI Clipboard or through MyNCBI in “My Collections” for later use are located at the right-hand end of this row along with the traditional “Links” menu that provides links to related information in other databases. Several of the more useful items from the “Links” menu are listed explicitly as Discovery column items described in the “Discovery Links” section below. The expandable display controls, “Change Region Shown” and “Customize View”, are located below the Links menu on the right-hand-side. The “Change Region Shown” control provides a convenient mechanism for displaying specific regions of the sequence. The “Customize View” control specifies the number and kinds of annotated features and the DNA strand that is shown.

 

Direct entry to analysis tools

The NCBI Discovery column begins just below the display controls with direct access to sequence analysis tools. The NCBI primer designing tool, Primer-BLAST (NCBI News, Nov 2008), is linked here now. Additional tools will be added in later versions of the viewer including a direct link to run a BLAST database search. In all cases these analysis tools are set in advance to provide the most relevant and up-to-date results appropriate to the context. For example, following the “Pick Primers” link from a human mRNA sequence in the viewer loads the Primer-BLAST form already set up to perform a specificity check against the appropriate background database, the human genome transcripts in this case. Moreover if the search is run with an older GenBank sequence as the query, the equivalent NCBI Reference Sequence (RefSeq) will be substituted to improve specificity checking. Direct access to analysis tools will streamline many visits to the NCBI Website by providing one-click, live access to the computing power of the NCBI.

Summary

The new Entrez sequence provides intuitive display controls, direct access to live analysis, and to the rich pre-compiled information available through Entrez Gene, OMIM and Homologene. The current version and future improvements move the sequence databases towards a condition where even older sequences become self-annotating and are automatically updated through the analysis performed at the NCBI evident in the Discovery column. These enhancements should make the NCBI Entrez system a more efficient experience for visitors and easier to use as a Discovery system.

New Databases and Tools

Genome Build

Build 1.1 of Hydra magnapapillata is available in the Genomes database and on the NCBI Map Viewer. The Map Viewer page is: www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=6085

Microbial Genomes

Twenty-eight finished microbial genomes were released between January 14 and February 6. The original sequence data files submitted to GenBank/EMBL/DDBJ are available on the FPT 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 170.0 is available via web and FTP. The current release includes information available as of February 13, 2009. With this release, the new DBLINK linetype is now legal for GenBank sequence records, and it will begin to appear in GenBank Update files, soon after GenBank 170.0 is made available. Release notes are on the on the ftp site: ftp.ncbi.nih.gov/genbank/gbrel.txt

Updates and Enhancements

Clone Finder

The Clone Finder tool, designed to identify genomic clones on a genome assembly, has been updated with an improved search interface that makes it easier to search by feature. Clone Finder also offers the ability to filter clones on results pages using feature information, and more informative pop-up menus on clone features. The performance of graphical view is improved and now integrates the library table view. The tool will now allow users to download all clones, or only clones from a given library in Excel format.

Documentation on Clone Finder can be found on the following Web page: www.ncbi.nlm.nih.gov/projects/mapview/static/clonefinder_documentation.shtml

UniVec

UniVec database build 5.1 is now available. UniVec is a non-redundant database of vector sequences used in conjunction with the VecScreen tool to identify vector sequence contamination in nucleotide sequences. The number of sequences in UniVec has increased by 2% for build 5.1. The vector BLAST database has also been updated to contain full-length versions of all sequences from GenBank that were used in the current UniVec build.

PubMed

The PubMed Summary page now displays information about free articles from publishers. The new information is in addition to the PubMed Central links that appear for full-text PMC articles. For more information, see the NLM Technical Bulletin article: www.nlm.nih.gov/pubs/techbull/jf09/jf09_pm_free_article.html . The current issue of the Technical Bulletin also has an informative article about shared settings in the My NCBI tool.

Exhibits

NCBI will have an exhibit booth at the Experimental Biology Annual Meeting on April 18-22 in New Orleans, Louisiana.

Announce Lists and RSS Feeds

Fifteen topic-specific mailing lists are described on the Announcement List summary page. Announce lists provide email announcements about changes and updates to NCBI resources. www.ncbi.nlm.nih.gov/Sitemap/Summary/email_lists.html

Seven 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/

Comments and questions about NCBI resources may be sent to NCBI at: This e-mail address is being protected from spambots. You need JavaScript enabled to view it , or by calling 301-496-2475 between the hours of 8:30 a.m. and 5:30 p.m. EST, Monday through Friday.

 

 

Last Updated on Saturday, 14 March 2009 22:06