A Practical Guide to NCBI Web and Standalone BLAST

12 May A Practical Guide to NCBI Web and Standalone BLAST

ITHS, the University of Washington Health Sciences Library, Fred Hutch, and the National Network of Libraries of Medicine, Pacific Northwest Region are pleased to host five free NLM National Center for Biotechnology Information (NCBI) workshops on June 14 and 15, 2016, in Seattle, Washington, and online.

This NCBI workshop highlights important features and demonstrates the practical aspects of using the NCBI BLAST service, the most popular sequence similarity service in the world. You will learn about useful but under-used features of the service. These include:

• Access from the Entrez sequence databases
• The new genome BLAST service quick finder
• The integration and expansion of Align-2-Sequences
• Organism limits and other filters
• Re-organized databases
• Formatting options and downloading options
• TreeView displays

You will also learn how to use other important sequence analysis services associated with BLAST including Primer BLAST, an oligonucleotide primer designer and specificity checker; the multiple protein sequence alignment tool, COBALT; IgBLAST, a tool for analysis of antibody and T-cell receptor sequences; and MOLE-BLAST, a new tool for clustering and providing taxonomic context for targeted loci sequences (16S, ITS, 28S). These aspects of BLAST provide easier access and results that are more comprehensive and easier to interpret. Finally, you will learn how to use the standalone VDB BLAST programs as clients to search whole genome shotgun contigs (WGS) and transcriptome shotgun assembly (TSA) data – two of the fastest growing categories of sequence data available for BLAST searching.

This session includes hands-on instruction.

Speaker Biography

Bonnie Maidack, PhD, is a member of the Public Services Section at NCBI and enjoys helping others learn how to use NCBI resources. She started her career path of biological information service while working on the OMIM database at Johns Hopkins Welch Medical Library in Baltimore, Maryland. Four years later, she moved to the Ribosomal Database Project (RDP) then located at UIUC and later at Michigan State University in East Lansing, Michigan and began curating prokaryotic ribosomal RNA sequence data. Bonnie relocated to Maryland approximately 15 years ago to start curating Reference Sequence Project data at NCBI, in Bethesda, Maryland. Bonnie Maidak  earned a B.S. in biology degree from Virginia Tech, a Ph.D. in medical genetics from Indiana University School of Medicine in Indianapolis, and a M.S. in Library and Information Sciences from the University of Illinois at Urbana-Champaign (UIUC).

Registration

There is no cost to attend this event, but seating is limited. Please register below if you plan to attend. Not an ITHS member? Signing up to become a member will take less than two minutes.