Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
Human Genome News, January 1994; 5(5)
The Informatics Group at Oak Ridge National Laboratory (ORNL) is making available several new sequence-analysis tools that operate within the distributed environment of genome resources. A major addition is genQuest ("Q" server), which uses such methods as Smith-Waterman, FastA, and BLAST to facilitate rapid and sensitive comparisons of DNA sequence and proteins in a number of databases. These databases include the Genome Sequence Database (GSDB) at Los Alamos National Laboratory (LANL), SWISS-PROT protein sequence database, PROSITE protein motif library, a human repetitive library provided by Jerzy Jurka (Linus Pauling Institute), Steve Henikoff's BLOCKS/BLIMPS resource, dbEST, IBM dFLASH server, and sequences in PDB protein/nucleic acid structure database. Future genQuest features will include capabilities for Smith-Waterman comparison of very long DNA sequences, multiple sequence alignment of DNA and proteins, methods for graphical visualization of sequence similarity, and a Macintosh client version. The genQuest server is accessible via e-mail and X-based client server.
The diagram (not shown here) shows the graphical client-server version of the main genQuest menu and use of the Smith-Waterman method to search for a partial protein sequence against SWISS-PROT and Prosite. The menu provides "point and click" options to specify sequence type, methods, and target databases. The client code runs on any Sun Sparc workstation having Internet access and communicates with the ORNL server system running on workstations and a parallel computer.
Significant improvements have also been made to GRAIL (Gene Recognition and Analysis Internet Link), a suite of tools that provides annotation of DNA sequences both interactively and through automated computation. GRAIL I and GRAIL II are available by several methods, including a simple e-mail interface that analyzes and characterizes coding regions in DNA sequences and returns results automatically by e-mail in a few minutes. New capabilities include comparison of discovered exons with the SWISS-PROT protein sequence database, Prosite, and the repetitive library. X-GRAIL, an interactive graphical X-based client-server system, is now capable of such functions as gene model construction, pol II promoter recognition, and repetitive element annotation. X-GRAIL also transparently accesses genQuest, furnishing additional capability for querying a multitude of databases for sequence comparison.
The Informatics Group plans to incorporate several tools that will provide sequence feature and map information for searches and databases as well as an easy-to-use menu-driven "glossary" for queries to a number of relational database systems. ORNL is also working with Richard Douthart (Pacific Northwest Laboratory) on a client-server version of GnomeView. Manesh Shah of the Informatics Group says, "Our goal is to provide an interoperable environment that allows users to ask a wide variety of questions about their sequence, ranging from sequence analysis to sequence comparison, and to access a variety of databases and other resources in a user-friendly manner. Our tools are designed to allow users without expert computer knowledge to interact with complex databases and analysis systems."
For instructions on using these resources, send an e-mail message with the word help in the subject line or first text line to:
Contact: Edward Uberbacher, Manesh Shah, Sergey Petrov, Xiaojun Guan, or Richard Mural; ORNL (firstname.lastname@example.org).
[Ed Uberbacher, ORNL]
The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v5n5).
The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.
Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.