DOI: 10.1007/11610496_129 Conference: Advanced Web and Network Technologies, and Applications, APWeb 2006 International Workshops: XRA, IWSN, MEGA, and ICSE, Harbin, China, January 16-18, 2006, Proceedings
In this work, an integrated Web-based model integrating a number of components has been proposed to analyze, manage and retrieve
biological information. In particular, we deal with Expressed Sequence Tags (EST) data that is an important resource for gene
identification, genome annotation and comparative genomics. A high-performance and user-friendly three-tier Web application
consisting of EST modeling and database (ESTMD) has been developed to facilitate the retrieval and analysis of EST information.
It provides a variety of Web services and tools for searching raw, cleaned and assembled EST sequences, genes and Gene Ontology,
as well as pathway information. It can be accessed at http://220.127.116.11:8080/estweb/index.html.
[Show abstract][Hide abstract] ABSTRACT: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the
networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of
biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway
information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different
organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms
with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes.
Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet.
In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing
biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression
profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).
Nucleic Acids Research 02/1999; 27(1):29-34. DOI:10.1093/nar/27.1.29 · 9.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users.
A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects.
The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http://titan.biotec.uiuc.edu/ESTIMA/. The entity-relationship (E-R) diagrams and the programs used to generate the Oracle database tables are also available. We have also provided detailed installation instructions and a tutorial at the same website. Presently the chromatograms, EST databases and their annotations have been made available for cattle and honeybee brain EST projects. Non-academic users need to contact the W.M. Keck Center for Functional and Comparative Genomics, University of Illinois at Urbana-Champaign, Urbana, IL, for licensing information.
[Show abstract][Hide abstract] ABSTRACT: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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