SeqHound: biological sequence and structure database as a platform for bioinformatics research

BMC Bioinformatics

Katerina Michalickova¹  Gary D Bader¹  Michel Dumontier¹  Hao Lieu¹  Doron Betel¹  Ruth Isserlin¹  Christopher WV Hogue¹ 

[1] Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5

关键词: local database resource;    structure database;    sequence database;   

Others  :  1171919
DOI  :  10.1186/1471-2105-3-32

 received in 2002-08-01, accepted in 2002-10-25,  发布年份 2002

【 摘 要 】

Background

SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment.

Results

SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries.

Conclusions

The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ webcite in the SLRI Toolkit.

【 授权许可】

   
2002 Michalickova et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.

【 图 表 】

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