DOE '99 Oakland Highlights
Meeting Intro
HGP Progress, Challenges
Joint Genome Institute
JGI Facility Opening
Sequencing
Device Speeds Sequencing
Chromosome 19 Genes
Functional Genomics
Sample Prep System
Informatics
Education & Bioethics
Microbial Genomes
Next Meeting Feb. 2000

Genome Project
Accelerated Timetable
FY1999 Budgets
JGI Refits Facility
Progress

In the News 
 Drosophila Near Completion
Directors, Researchers Receive Awards
Chromosomes 21, 22 Near Finish
Human MHC Region Sequenced
Mouse Probes Aid Mapping
Genetic Testing Committee
DOE Labs & Biomedicine
Biomedical Engineering Proposals
Drug Firms Create SNP Resource
SBIR 1999 Awards
HUGO News
1999 Hollaender Winners

Microbial Genomics 
EcoCyc Database for E. coli
Developing EcoCyc
Thermotoga Sequence
Clostridium Sequenced
Microbial Gene Finder
Neisseria Sequence
Microbial Web Sites

Ethical, Legal, and Social Issues
Education, Counseling Foundation
 ELSI Studies
ELSI Retrospective
Protecting Privacy

Informatics 
MGI 2.2 Released
DNA Repository

Web, Other Resources, Publications 
Metabolic Pathways
New Staden Package
PDB Newsletter
Polymorphism Database
Bacterial Protein Database
DOE BER Publications
HGP Information Web
Biotechnology Business Webs
Behavioral Genetics
Office of Science Reports
Articles on Genetics

Funding 
Genome Research Funding

Meeting Calendars & Acronyms 
Genome & Biotech Meetings 
Training Courses & Workshops 
Acronyms 

HGN archives & subscriptions 
HGP Information home

Resources

New Staden Package Released

Release 1999.0 of the Staden Package from the MRC Laboratory of Molecular Biology (Cambridge, U.K.) incorporates the new PREGAP4 program, which has a graphical user interface and a batch mode (www.mrc-lmb.cam.ac.uk/pubseq). Used to prepare sequences for assembly, PREGAP4 includes trace file conversion, vector and quality clipping, contaminant screening, repeat masking, and batch-mode assembly via such programs as Phrap, FAKII, CAP3, and GAP4. New algorithms increase VECTOR_CLIP's sensitivity and flexibility, and the new SCREEN_SEQ program filters readings contaminated with Escherichia coli or yeast.

Besides bug fixes, the GAP4 program has many additions. The trace display includes a multicolumn format, which by use of a vertical scrollbar can show any number of traces. The "auto-display-traces" mode works for more search types, and the search for contig joins is more sensitive. The maximum reading length is increased from 4096 to 30,000bases, and a "notes" data type stores notebook-style comments about readings, contigs, and databases. The contig editor displays the confidence for the bases in the readings and in the consensus. "Sort Matches" is applied automatically for several commands, and matches are processed in order of their significance. GAP4 includes interfaces to Phrap, FAKII, and CAP3. NIP4 and SIP4 provide improved sequence library browsing using SRS indexes.

The CD-ROM containing package versions for Solaris, Digital Unix, IRIX, and Linux is free to academic sites. Courses on using the package are announced on the Web site.

The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v10n3-4).