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Human Genome News Archive Edition
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  Vol.10, No.1-2   February 1999

In this issue...

Available in PDF

Genome Project

In the News

Microbial Genomics

Ethical, Legal, and Social Issues and Educational Resources


Genetics in Medicine


Web, Other Resources, Publications


Meeting Calendars & Acronyms

  • Genome and Biotechnology Meetings
  • Training Courses and Workshops
  • Acronyms

HGN archives and subscriptions

Human Genome Project Information home

Database Information

Influenza Database at LANL

Los Alamos National Laboratory (LANL) introduced its annotated Influenza Sequence Database [http://www.flu.lanl.gov/] 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currently holds all the influenza sequences published in GenBank and, after verification and annotation, will add unpublished sequences collected around the world.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.


The TRANSFAC database [http://www.gene-regulation.com/pub/databases.html] 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 [http://www.gene-regulation.com/pub/databases/transfac/cl.html] 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. (info@biobase-international.com).

[TRANSFAC contact: 800/305-0670, Germany +49-531/6181-427; http://www.biobase-international.com/contact]

p53 Mutation Database

The p53 mutation database [http://p53.iarc.fr/] contains information on all p53 missense mutations and small deletions in human tumors and cell lines as reported in peer-reviewed literature.

TBASE at Jackson Laboratory

TBASE, the database of transgenic animals and targeted mutations, is at the Jackson Laboratory in Bar Harbor, Maine. (http://www.informatics.jax.org/; tbase@jax.org)

Intein Database on Web

The Intein Database Web site [http://www.neb.com/neb/inteins.html] contains a registry of all submitted experimental and theoretical inteins (inframe protein introns) as well as information on protein splicing and intein structure.

The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v10n1-2).

Human Genome Project 1990–2003

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.

Human Genome News

Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.