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Here, we present PatMatch, an efficient, web-basedpattern-matching program that enables searches forshort nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domainsandmotifsinproteinsequences.Theprogramcanbeused to find matches to a user-specified sequencepattern that can be described using ambiguoussequence codes and a powerful and flexible patternsyntax based on regular expressions. A recentupgrade has improved performance and nowsupports both mismatches and wildcards in a singlepattern. This enhancement has been achievedbyreplacingtheprevioussearchingalgorithm,scan_for_matches [D’Souza et al. (1997), Trends inGenetics, 13, 497–498], with nondeterministic-reverse grep (NR-grep), a general pattern matchingtool that allows for approximate string matching[Navarro (2001), Software Practice and Experience,31, 1265–1312]. We have tailored NR-grep to beused for DNA and protein searches with PatMatch.The stand-alone version of the software can beadapted for use with any sequence dataset and isavailable for download at The Arabidopsis Infor-mation Resource (TAIR) at ftp://ftp.arabidopsis.org/home/tair/Software/Patmatch/. The PatMatch serveris available on the web at http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl for searchingArabidopsis thaliana sequences.INTRODUCTIONPatMatch is designed to find short (3–30 nt or amino acid)sequence matches. It can be useful for finding short patternsin nucleotide sequences such as cis-elements, massivelyparallel signature sequence (MPSS), instances of known serialanalysis of gene expression (SAGE) tags, small RNA bindingsitesorsmallproteindomainsandmotifsinproteinsequences.PatMatch uses a short sequence or regular expression asinput and allows ambiguous sequences to be represented bystandard International Union of Pure and Applied Chemistry(IUPAC; http://www.chem.qmw.ac.uk/iupac) nomenclature.The program also allows inexact matching (mismatches)of the query sequence against literal or regular expres-sion patterns. PatMatch requires users to explicitly enter apattern to search for and is not meant for de novo patterndetection.The original version of PatMatch was provided by theSaccharomyces Genome Database (SGD; http://www.yeastgenome.org/) (1) and was modified to be deployed atThe Arabidopsis information resource (2,3). In this paper,we report on changes we made to the software to improveperformance and support for mismatches when usingwildcards in the query sequence by using Nondeterministic-Reverse grep (NR-grep) (4). In addition, the CommonGateway Interface (CGI) code has been restructured, andthe auxiliary programs that displayed the results, whichwere written in C, were rewritten in Perl and modularizedto facilitate maintenance and future extension. This newversion of PatMatch is available at TAIR and is also availablefrom SGD at http://db.yeastgenome.org/cgi-bin/PATMATCH/nph-patmatch. more...

Controlled vocabularies are increasingly used by databases to describe genes and gene products because they facilitate identification of similar genes within an organism or among different organisms. One of The Arabidopsis Information Resource's goals is to associate all Arabidopsis genes with terms developed by the Gene Ontology Consortium that describe the molecular function, biological process, and subcellular location of a gene product. We have also developed terms describing Arabidopsis anatomy and developmental stages and use these to annotate published gene expression data. As of March 2004, we used computational and manual annotation methods to make 85,666 annotations representing 26,624 unique loci. We focus on associating genes to controlled vocabulary terms based on experimental data from the literature and use The Arabidopsis Information Resource-developed PubSearch software to facilitate this process. Each annotation is tagged with a combination of evidence codes, evidence descriptions, and references that provide a robust means to assess data quality. Annotation of all Arabidopsis genes will allow quantitative comparisons between sets of genes derived from sources such as microarray experiments. The Arabidopsis annotation data will also facilitate annotation of newly sequenced plant genomes by using sequence similarity to transfer annotations to homologous genes. In addition, complete and up-to-date annotations will make unknown genes easy to identify and target for experimentation. Here, we describe the process of Arabidopsis functional annotation using a variety of data sources and illustrate several ways in which this information can be accessed and used to infer knowledge about Arabidopsis and other plant species. more...

Arabidopsis thaliana is the most widely-studied plant today. The concerted efforts of over 11 000 researchers and 4000 organizations around the world are generating a rich diversity and quantity of information and materials. This information is made available through a comprehensive on-line resource called the Arabidopsis Information Resource (TAIR) (http://arabidopsis.org), which is accessible via commonly used web browsers and can be searched and downloaded in a number of ways. In the last two years, efforts have been focused on increasing data content and diversity, functionally annotating genes and gene products with controlled vocabularies, and improving data retrieval, analysis and visualization tools. New information include sequence polymorphisms including alleles, germplasms and phenotypes, Gene Ontology annotations, gene families, protein information, metabolic pathways, gene expression data from microarray experiments and seed and DNA stocks. New data visualization and analysis tools include SeqViewer, which interactively displays the genome from the whole chromosome down to 10 kb of nucleotide sequence and AraCyc, a metabolic pathway database and map tool that allows overlaying expression data onto the pathway diagrams. Finally, we have recently incorporated seed and DNA stock information from the Arabidopsis Biological Resource Center (ABRC) and implemented a shopping-cart style on-line ordering system. more...

The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) provides an integrated view of genomic data for Arabidopsis thaliana. The information is obtained from a battery of sources, including the Arabidopsis user community, the literature, and the major genome centers. Currently TAIR provides information about genes, markers, polymorphisms, maps, sequences, clones, DNA and seed stocks, gene families and proteins. In addition, users can find Arabidopsis publications and information about Arabidopsis researchers. Our emphasis is now on incorporating functional annotations of genes and gene products, genome-wide expression, and biochemical pathway data. Among the tools developed at TAIR, the most notable is the Sequence Viewer, which displays gene annotation, clones, transcripts, markers and polymorphisms on the Arabidopsis genome, and allows zooming in to the nucleotide level. A tool recently released is AraCyc, which is designed for visualization of biochemical pathways. We are also developing tools to extract information from the literature in a systematic way, and building controlled vocabularies to describe biological concepts in collaboration with other database groups. A significant new feature is the integration of the ABRC database functions and stock ordering system, which allows users to place orders for seed and DNA stocks directly from the TAIR site. more...