An effective approach for analyzing "prefinished" genomic sequence data.
Ongoing efforts to sequence the human genome are already generating large amounts of data, with substantial increases anticipated over the next few years. In most cases, a shotgun sequencing strategy is being used, which rapidly yields most of the primary sequence in incompletely assembled sequence contigs ("prefinished" sequence) and more slowly produces the final, completely assembled sequence ("finished" sequence). Thus, in general, prefinished sequence is produced in excess of finished sequence, and this trend is certain to continue and even accelerate over the next few years. Even at a prefinished stage, genomic sequence represents a rich source of important biological information that is of great interest to many investigators. However, analyzing such data is a challenging and daunting task, both because of its sheer volume and because it can change on a day-by-day basis. To facilitate the discovery and characterization of genes and other important elements within prefinished sequence, we have developed an analytical strategy and system that uses readily available software tools in new combinations. Implementation of this strategy for the analysis of prefinished sequence data from human chromosome 7 has demonstrated that this is a convenient, inexpensive, and extensible solution to the problem of analyzing the large amounts of preliminary data being produced by large-scale sequencing efforts. Our approach is accessible to any investigator who wishes to assimilate additional information about particular sequence data en route to developing richer annotations of a finished sequence. (+info
The Genexpress IMAGE knowledge base of the human brain transcriptome: a prototype integrated resource for functional and computational genomics.
Expression profiles of 5058 human gene transcripts represented by an array of 7451 clones from the first IMAGE Consortium cDNA library from infant brain have been collected by semiquantitative hybridization of the array with complex probes derived by reverse transcription of mRNA from brain and five other human tissues. Twenty-one percent of the clones corresponded to transcripts that could be classified in general categories of low, moderate, or high abundance. These expression profiles were integrated with cDNA clone and sequence clustering and gene mapping information from an upgraded version of the Genexpress Index. For seven gene transcripts found to be transcribed preferentially or specifically in brain, the expression profiles were confirmed by Northern blot analyses of mRNA from eight adult and four fetal tissues, and 15 distinct regions of brain. In four instances, further documentation of the sites of expression was obtained by in situ hybridization of rat-brain tissue sections. A systematic effort was undertaken to further integrate available cytogenetic, genetic, physical, and genic map informations through radiation-hybrid mapping to provide a unique validated map location for each of these genes in relation to the disease map. The resulting Genexpress IMAGE Knowledge Base is illustrated by five examples presented in the printed article with additional data available on a dedicated Web site at the address http://idefix.upr420.vjf.cnrs.fr/EXPR++ +/ welcome.html. (+info
International travel and vaccinations.
With the increase in global travel, no disease is beyond the reach of any population. Traveling patients should be advised to follow food and water precautions and encouraged to receive the recommended immunizations. Travel medicine plays a vital role not only in limiting the morbidity of travel-related illnesses but also in limiting the spread of diseases. This article addresses the common issues related to travel, reviews the care of the immunocompromised traveler, and updates the available vaccinations and prophylactic regimens available to limit sickness abroad. (+info
A World Wide Web selected bibliography for pediatric infectious diseases.
A pediatric infectious diseases bibliography of selected medical reference citations has been developed and placed on the World Wide Web (WWW) at http://www.pedid.uthscsa.edu. A regularly updated bibliography of >2,500 selected literature citations representing general reviews and key articles has been organized under a standard outline for individual infectious diseases and related topics that cover the breadth of pediatric infectious diseases. Citations are categorized by infectious disease or clinical syndrome, and access can be achieved by the disease or by syndrome or the name of the pathogen. Abstracts, and in some cases the complete text of articles, may be viewed by use of hypertext links. The bibliography provides medical students, residents, fellows, and clinicians with a constantly available resource of current literature citations in pediatric infectious diseases. The WWW is an emerging educational and clinical resource for the practice of clinical infectious diseases. (+info
Published criteria for evaluating health related web sites: review.
OBJECTIVE: To review published criteria for specifically evaluating health related information on the world wide web, and to identify areas of consensus. DESIGN: Search of world wide web sites and peer reviewed medical journals for explicit criteria for evaluating health related information on the web, using Medline and Lexis-Nexis databases, and the following internet search engines: Yahoo!, Excite, Altavista, Webcrawler, HotBot, Infoseek, Magellan Internet Guide, and Lycos. Criteria were extracted and grouped into categories. RESULTS: 29 published rating tools and journal articles were identified that had explicit criteria for assessing health related web sites. Of the 165 criteria extracted from these tools and articles, 132 (80%) were grouped under one of 12 specific categories and 33 (20%) were grouped as miscellaneous because they lacked specificity or were unique. The most frequently cited criteria were those dealing with content, design and aesthetics of site, disclosure of authors, sponsors, or developers, currency of information (includes frequency of update, freshness, maintenance of site), authority of source, ease of use, and accessibility and availability. CONCLUSIONS: Results suggest that many authors agree on key criteria for evaluating health related web sites, and that efforts to develop consensus criteria may be helpful. The next step is to identify and assess a clear, simple set of consensus criteria that the general public can understand and use. (+info
Genetic Simulation Library.
SUMMARY: The Genetic Simulation Library (GSL) is a set of C++ programs and classes that can be used in individual-based simulation models of plant and animal populations. The classes in this library build representations of genes for a wide variety of different types of organisms, from asexually reproducing single-cell organisms to chromosome-structured sexually reproducing species. AVAILABILITY: http://www.csi.uoregon.edu/projects/genetics/GSL . Free for non-commercial applications; others should contact the author. (+info
Application of distance geometry to 3D visualization of sequence relationships.
SUMMARY: We describe the application of distance geometry methods to the three-dimensional visualization of sequence relationships, with examples for mumps virus SH gene cDNA and prion protein sequences. Sequence-sequence distance measures may be obtained from either a multiple sequence alignment or from sets of pairwise alignments. AVAILABILITY: C/Perl code and HTML/VRML files from http://www.nibsc.ac.uk/dg3dseq/ (+info
An extensive list of genes that produce alternative transcripts in the mouse.
SUMMARY: A single gene can generate multiple transcribed gene products. An extensive list of alternatively transcribed mouse genes has been generated, and is publicly available from http://www.informatics.jax.org/report.html. CONTACT: [email protected]