Ulcerative colitis (UC) is a common form of inflammatory bowel disease with a complex aetiology. As part of the Wellcome Trust Case Control Consortium 2, we performed a genomewide association scan for UC in 2361 cases and 5417 controls. Loci showing evidence of association at P < 1 × 10 −5 were followed up by genotyping in an independent set of 2321 cases and 4818 controls. We find genome-wide significant evidence of association at three new loci, each containing at least one biologically relevant candidate gene, on chromosomes 20q13 (HNF4A; P = 3.2 × 10 −17 ), 16q22 (CDH1 and CDH3; P = 2.8 × 10 −8 ) and 7q31 (LAMB1; 3.0 × 10 −8 ). Of note, CDH1 has recently been associated with susceptibility to colorectal cancer, which is an established complication of longstanding UC. The new associations suggest that changes in the integrity of the intestinal epithelial barrier may contribute to the pathogenesis of UC.

The BCM Search Launcher is an integrated set of World Wide Web (WWW} pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point of entry for related searches. The Protein Sequence Search Page, for example, provides a single sequence entry form for submitting sequences to WWW servers that offer remote access to a variety of different protein sequence search tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, PROSITE, and BLOCKS searches. Other Launch pages provide access to {I) nucleic acid sequence searches, (2} multiple and pair-wise sequence alignments, (3} gene feature searches, (4} protein secondary structure prediction, and (5) miscellaneous sequence utilities (e.g., six-frame translation). The BCM Search Launcher also provides a mechanism to extend the utility of other WWW services by adding supplementary hypertext links to results returned by remote servers. For example, links to the NCBI's Entrez data base and to the Sequence Retrieval System (SRS) are added to search results returned by the NCBI's WWW BLAST server. These links provide easy access to auxiliary information, such as Medline abstracts, that can be extremely helpful when analyzing BLAST data base hits. For new or infrequent users of sequence data base search tools, we have preset the default search parameters to provide the most informative first-pass sequence analysis possible. We have also developed a batch client interface for Unix and Macintosh computers that allows multiple input sequences to be searched automatically as a background task, with the results returned as individual HTML documents directly to the user's system. The BCM Search Launcher and batch client are available on the WWW at URL http://gc.bcm.tmc.edu:8088/search-launcher.html.DNA and protein sequence analysis services are now available from a large number of sources on the Internet, including Email, Gopher, and World Wide Web (WWW) servers (for review, see Boguski 1994;Harper 1994). These services are extremely useful for molecular biologists, as they allow access to the ever-expanding sequence data bases without requiring copious local data base storage, frequent data base updates, the cost of expensive and sophisticated hardware and software, and the cost and effort of continuous system maintenance.The development of the WWW, a hypertext- multimedia communications system on the Internet, has been particularly useful in making international biological resources readily available and more easy to use (Jacobson 1994;Harper 1995;Schatz and Hardin 1994). Analysis results returned by WWW servers are easy to view (one can move forward and backward through a document using slider bars), and a hypertext document can include any number of hypertext links, allowing direct access to a variety of additional information sources on the Internet (e.g., related documents and other services). Although comprehensive lists of molecular biology-related search and analysis resources currently available on the W...

Several efforts are under way to partition single-read expressed sequence tag (EST), as well as full-length transcript data, into large-scale gene indices, where transcripts are in common index classes if and only if they share a common progenitor gene. Accurate gene indexing facilitates gene expression studies, as well as inexpensive and early gene sequence discovery through assembly of ESTs that are derived from genes that have not been sequenced by classical methods. We extend, correct, and enhance the information obtained from index groups by splitting index classes into subclasses based on sequence dissimilarity (diversity). Two applications of this are highlighted in this report. First it is shown that our method can ameliorate the damage that artifacts, such as chimerism, inflict on index integrity. Additionally, we demonstrate how the organization imposed by an effective subpartition can greatly increase the sensitivity of gene expression studies by accounting for the existence and tissue-or pathology-specific regulation of novel gene isoforms and polymorphisms. We apply our subpartitioning treatment to the UniGene gene indexing project to measure a marked increase in information quality and abundance (in terms of assembly length and insertion/deletion error) after treatment and demonstrate cases where new levels of information concerning differential expression of alternate gene forms, such as regulated alternative splicing, are discovered.