SeqHound
Subtitle: an integrated bioinformatics resource and its applications.
Published: 2005
Language: eng
Number of pages: 278
Description: SeqHound is an integrated bioinformatics database system. SeqHound provides a resource of basic biological information and enables hypothesis driven bioinformatics research. The system facilitates simple, uniform and automated access to various biological data resources. It offers daily updated contents of all Entrez sequence databases, 3-D structural data and annotation. SeqHound holds links from sequences to sequence neighbours, equivalent sequences from other sources, 3-D structures, structural domains, taxonomy, complete genomes and functional annotation including Gene Ontology terms and literature links to PubMed. Currently, the SeqHound data collection is being enriched with molecule interaction data, literature mining data and an extensive collection of sequence identifiers from assorted specialized databases.SeqHound provides the functionality necessary to retrieve sequences, structures and structural domains using numerous entry points for querying. It is accessible via a web server through a remote Application Programming Interface (API) in Perl, Bioperl, Java, C or C++ programming languages or directly through an optimized local C API. The system is based on the National Center for Biotechnology Information data model and programming tools and offers equivalent functionality in terms of available data formats. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats.The data held by SeqHound can be a starting point for any bioinformatics application. If an application or calculation is to be performed on an on-going basis, the underlying data must also be regularly updated. SeqHound removes the burden of keeping data up to date from the researcher allowing them to focus on developing their bioinformatics analysis. Several published applications ranging from lightweight GUI interfaces to robust data analysis applications were built using SeqHound. The thesis presents a family of species-specific scoring functions, PreBIND, BIND, FAST, Kangaroo and MMDBind systems and explains the way they utilize SeqHound.
Notes: Thesis (Ph.D.)--University of Toronto, 2005.

Electronic version licensed for access by U. of T. users.

Source: Dissertation Abstracts International, Volume: 66-06, Section: B, page: 3118.