Generic Model Organism Database Construction Set

LuceGene: Document/Object Search and Retrieval for Genome Databases

This is an open-source document/object search and retrieval system specially tuned for bioinformatics text databases and documents. LuceGene is similar in concept to the widely used, commercially successful, bioinformatics program SRS (Sequence Retrieval System).

It is built with the open-source Lucene package. It includes common text search features: booleans, phrases, word stemming, fuzzy and field range searches, relevance ranking. It supports data field structure of many kinds. Lucene is comparable to web-indexing systems such as Exite, Alta-vista, and Google. LuceGene adds these bio-data methods to Lucene:

  • Indexing adaptors for formats such as XML, PDF Documents, Biosequences, Spreadsheets, HTML, and others.
  • Configurations for bio-data include UniProt/Swiss-Prot, Fasta and GenBank sequences, BIND protein interactions, NCBI Gene Expression Omnibus, BLAST output tables, Medline.
  • Support for batch-list look-ups and searches is included, useful for data miners.
  • Web applications offer paged search results, batch downloads, search refinement and search-linking among data libraries.
  • Web Services support for data mining is included with a SOAP interface.
  • Output support includes field selection and formats such as Spreadsheet, XML, HTML via XSLT, and others.

    LuceGene is speedy with big data sets: Searching the UniProt library of 1.7 million sequences with LuceGene is a close equivalent to SRS in speed and content. Gene Annotation object search and retrieval with LuceGene is 10x to 20x faster than using a Postgres Chado database. LuceGene has been tested and works well with millions of documents from genome sequence, annotation and literature databases.

    Demo & Screenshots
  • Demo Screenshots
  • Demonstration server is available at
  • FlyBase Search preview
  • euGenes genome search
  • Daphnia/wFleaBase search

  • LuceGene requires Java versions 1.4 or later to compile and run.
  • A Java/JSP web server like Jakarta Tomcat is used for the web application.
    Jakarta Lucene software is included with this package, as are other required java libraries.

  • LuceGene Readme
  • INSTALL.txt for demo webapp use
  • Indexing methods overview
  • Talk slides on Argos/LuceGene, Sept 2003: PowerPoint PDF

    Current distribution files are at SourceForge and
  • lucegene.war : web application archive
  • lucegene-*-src.jar : sources, documents, configurations
  • sample data for lucegene.war as lucegene_demo*.zip

    email: lucegene AT
    Current developers: Don Gilbert, Paul Poole, and others