Human Genome Project Information Archive
1990–2003

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the new PREGAP4 program, which has a graphical user interface and a batch mode (www.mrc-lmb.cam.ac.uk/pubseq [url no longer active]). 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).