title: HitKeeper, a generic software package for hit list management.
abstract: BACKGROUND
  The automated annotation of biological sequences (protein, DNA) relies on the computation of hits (predicted features) on the sequences using various algorithms. Public databases of biological sequences provide a wealth of biological "knowledge", for example manually validated annotations (features) that are located on the sequences, but mining the sequence annotations and especially the predicted and curated features requires dedicated tools. Due to the heterogeneity and diversity of the biological information, it is difficult to handle redundancy, frequent updates, taxonomic information and "private" data together with computational algorithms in a common workflow.
  
  
  RESULTS
  We present HitKeeper, a software package that controls the fully automatic handling of multiple biological databases and of hit list calculations on a large scale. The software implements an asynchronous update system that introduces updates and computes hits as soon as new data become available. A query interface enables the user to search sequences by specifying constraints, such as retrieving sequences that contain specific motifs, or a defined arrangement of motifs ("metamotifs"), or filtering based on the taxonomic classification of a sequence.
  
  
  CONCLUSIONS
  The software provides a generic and modular framework to handle the redundancy and incremental updates of biological databases, and an original query language. It is published under the terms and conditions of version 2 of the GNU Public License and available at http://hitkeeper.sourceforge.net.
authors: Swiss Institute of Bioinformatics, Vital-IT group, CH-1015 Lausanne, Switzerland. joerg.hau@rdls.nestle.com
authors: Jörg
authors: J
authors: Hau
authors: Michael
authors: M
authors: Muller
authors: Marco
authors: M
authors: Pagni