News from April 2013
New publication: "BLAST: a more efficient report with usability improvements."
A new publication, "BLAST: a more efficient report with usability improvements," (PMID: 23609542) is now available in free full-text from the Webserver Issue of Nucleic Acids Research. The paper describes the recent improvements in the NCBI BLAST Web output. These include more efficient loading of results, the ability to retrieve only the aligned regions, to display query-based or subject-based views of results in the graphical sequence viewer and to customize the descriptions table. A factsheet and a video on the NCBI YouTube channel provide a practical introduction to these features.
"A Librarian's Guide to NCBI" Course was a Success!
Last week (April 15-19, 2013), NCBI in collaboration with the National Library of Medicine and the National Network of Libraries of Medicine NLM Training Center at the University of Utah presented "A Librarian’s Guide to NCBI". This new course, which was highly rated by participants, was designed to prepare health science librarians for supporting and training patrons about NCBI molecular databases and tools at their own institutions.
As promised in last week’s NCBI Insights Blog post, the materials used in "A Librarian's Guide to NCBI" are now available for download and use for personal enlightenment or to supplement training in workshops or courses.
GenBank Release 195.0 is Available
The new release for GenBank is now available via ftp.ncbi.nlm.nih.gov, as well as in the Nucleotide database and BLAST services.
New Educational Initiative: A Librarian's Guide to NCBI
Next week NCBI will premiere A Librarian’s Guide to NCBI, a new course aimed at teaching health science librarians about NCBI resources. For more information, a new NCBI Insights Blog introduces the course and updates on the course and the availability of the curricular materials will be publicized on Twitter and Facebook.
PubChem Releases New and Enhanced Webpage Widgets
New PubChem Widgets (Chemical Structure Carousel, Classification Listing and Autocomplete) have been developed for you to use in your own webpage. In addition, existing table-based Widgets (including Bioactivity, Patents and PubMed) have been enhanced with a Link/Embed button that allows you to open the widget in a PubChem page or embed the widget in your own page as an iframe.
BLAST 2.2.28 now available
Stand-alone BLAST version 2.2.28+ is now available for download from the FTP site. BLAST 2.2.28+ provides a number of important new features, improvements and some bug fixes. New features include composition-based statistics for Reverse PSI-BLAST (rpsblast), expanded options (query coverage, subject title, and taxonomy) for tabular output, and batch subsequence retrieval in blastdbcmd. Improvements include adaptive BATCH_SIZE resulting in more efficient searching, and incremental production of XML results. The Blast Release Notes have more details.
Try it out! The New PubChem Upload Beta Site
A new beta version PubChem Upload system is available to try out. It features streamlined procedures for data submissions and updates to both the PubChem Substance and BioAssay databases.
New database options in Microbial Genomes BLAST: Representative Genomes
Microbial Genomes BLAST has new database options including 'Representative genomes', now the default database, and 'All genomes'. Representative genomes provide a smaller less redundant set of records for a given bacterial species. These representatives are selected by the research community and NCBI computational processes and are especially helpful for microbial species that are highly represented by genomes for numerous strains in NCBI databases, such as Escherichia coli. The 'All genomes' option offers the choice of Complete genomes, Draft genomes, or Complete plasmids. You can search these sets individually or in any combination. The microbial BLAST report also has a new 'Genome' link to the species page in Entrez Genome in the alignments section of the BLAST report. Run a search.