SeqHound

SeqHound provides an integrated database and retrieval system for biological sequences, taxonomy, functional annotations, and 3-D structure data, aggregating daily-updated contents from Entrez sequence databases.

Key Features:

• 3-D Structural Data: Access to 3-D structures with outputs available in PDB, ASN.1, and XML formats.
• Sequence Data and Formats: Sequence retrieval in FASTA, GenBank, ASN.1, and XML formats.
• Entrez Integration: Integration of daily-updated contents from all Entrez sequence databases.
• Taxonomy and Complete Genomes: Provision of taxonomy details and complete genome datasets.
• Redundancy and Neighbor Information: Identification and reporting of sequence redundancies and neighbor relationships.
• Functional Annotation: Storage and retrieval of functional annotations including Gene Ontology terms.
• Literature Links: Links between sequences/annotations and PubMed literature entries.
• Programmatic APIs: Remote APIs in Perl, C, and C++ and an optimized local API for retrieving specialized subsets of sequences, structures, and structural domains.
• NCBI Data Model: Implementation based on the NCBI data model and programming tools.

Scientific Applications:

• BIND Database Support: Used to support the BIND database by providing integrated sequence, annotation, and structural data.
• Integrated Bioinformatics Projects: Supports projects requiring coordinated access to sequences, taxonomy, functional annotations, 3-D structures, and literature links.

Methodology:

Built on the NCBI data model and programming tools; integrates daily updates from Entrez sequence databases; serves sequences in FASTA, GenBank, ASN.1, and XML and structures in ASN.1, XML, and PDB; exposes remote APIs in Perl, C, and C++ and an optimized local API for specialized subset retrieval.