PEDANT covers all complete RefSeq genomes.

The PEDANT genome database provides exhaustive annotation of nearly 3000 publicly available eukaryotic, eubacterial, archaeal and viral genomes with more than 4.5 million proteins by a broad set of bioinformatics algorithms. In particular, all completely sequenced genomes from the NCBI's Reference Sequence collection (RefSeq) are covered. The PEDANT processing pipeline has been sped up by an order of magnitude through the utilization of precalculated similarity information stored in the similarity matrix of proteins (SIMAP) database, making it possible to process newly sequenced genomes immediately as they become available. PEDANT is freely accessible to academic users at http://pedant.gsf.de. For programmatic access Web Services are available at http://pedant.gsf.de/webservices.jsp.

Acceptance of and attitude toward genetic testing for hereditary nonpolyposis colorectal cancer: a comparison of participants and nonparticipants in genetic counseling.

PURPOSE: Data on the actual uptake of genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC) in a clinical sample is still inconclusive. The present study aimed to define the actual uptake of genetic counseling and testing offered to an unselected sample of 140 patients with colorectal cancer, fulfilling clinical criteria (Amsterdam or Bethesda) suggestive of HNPCC, and to identify demographic and psychosocial factors associated with the decision to participate in counseling. METHODS: Cross-sectional survey. Eligible subjects had been consecutively enrolled in a regional tumor registry between 1994 and 1998, and were invited to attend an information session for HNPCC at the time genetic testing for HNPCC became available. Participants and nonparticipants in the information session completed a short questionnaire. RESULTS: The actual uptake rate of the information session in this sample was 26 percent. Participants and nonparticipants were comparable with regard to clinical criteria suggestive of HNPCC, awareness of the potential hereditary predisposition, and previous history of cancer in the family. Some 60 percent of participants experienced pronounced distress related to their potential inheritance of the disorder, compared to 35 percent among nonparticipants. Distress reached a clinically significant level in 28 percent of participants. Restricted communication within the family was observed frequently. Irrespective of groups, a positive attitude toward obtaining a gene test result predominated. CONCLUSIONS: Results suggest that expressed intention and attitude toward genetic testing do not reliably predict actual uptake of counseling or testing. Thorough interdisciplinary counseling should be provided to every patient with clinical criteria suggestive of HNPCC. The considerable distress related to the hereditary disorder should be adequately addressed, as should be communication issues.

ARB: a software environment for sequence data.

The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design and evaluation and other components for data analysis. Currently, the package is used by numerous working groups worldwide.