Progress, and Applications
of the Human Genome Project
Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
In this issue...
In the News
Genetics in Medicine
Los Alamos National Laboratory (LANL) introduced its annotated Influenza Sequence Database in July 1998. The database currently holds all the influenza sequences published in GenBank and, after verification and annotation, will add unpublished sequences collected around the world. LANL is working with the University of California and the Centers for Disease Control and Prevention to expand the database.
TRANSFAC database compiles data about gene regulatory DNA sequences and protein factors binding to them. Programs help identify putative promoter or enhancer structures and suggest their features.
TRANSFAC consists of six cross-linked tables: SITE, CELL, FACTOR, CLASS, MATRIX, and GENE. FACTOR entries also are cross-linked with a proposed classification system for transcription factors. TRANSFAC is linked to a number of other databases. Among the most recent additions are enhanced internal hyperlinking between individual tables, improved linking of references to PubMed, and insertion of most training sequence sets used for matrix construction, including the corresponding site-matrix links.
The TRANSFAC server also provides access to such sequence-analysis tools as PatternSearch, which uses sequence information contained in the SITE table for analysis of submitted sequences; and MatInspector, which uses a library of matrices selected from the TRANSFAC MATRIX table. Another sequence-analysis program, FastM, developed by the group of Thomas Werner (National Research Centre for Environment and Health, Neuherberg), is included on the TRANSFAC server. Using the MatInspector algorithm, FastM analyzes sequences for user-defined combinations of transcription factor-binding sites. The Structural Analysis with Genetic Algorithms (SaGa) program can identify structural characteristics in the environment of aligned functional sites.
TRANSFAC tools are freely accessible for users from noncommercial organizations. Users from profit-oriented organizations are requested to obtain licensing from BIOBASE Ltd. (email@example.com).
[TRANSFAC contact: Edgar Wingender (+49-531/6181-427, Fax: -266, firstname.lastname@example.org)]
database contains information on all p53 missense mutations and small deletions in human tumors and cell lines as reported in peer-reviewed literature.
TBASE, the database of transgenic animals and targeted mutations, is at the Jackson Laboratory in Bar Harbor, Maine (email@example.com).
Web site contains a registry of all submitted experimental and theoretical inteins (inframe protein introns) as well as information on protein splicing and intein structure.
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Last modified: Monday, December 15, 2003
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