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IMDB: A Generic Insertional Mutagenesis Database

IMDB: A Generic Insertional Mutagenesis Database. Xiaokang Pan and Lincoln Stein Cold Spring Harbor Laboratory. Objectives. Store sequenced insertion sites for model organisms

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IMDB: A Generic Insertional Mutagenesis Database

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  1. IMDB: A Generic Insertional Mutagenesis Database Xiaokang Pan and Lincoln Stein Cold Spring Harbor Laboratory

  2. Objectives • Store sequenced insertion sites for model organisms • Provide users with useful tools to search for insertions in gene of interest and to track progress of the multinational effort to find insertions in each gene. • Facilitate the study of insertion site distributions

  3. Insertion Mapping Flanking sequence TIGR pseudo-chromosomes WU-BLAST If the top hit with score > 90 TIGR genome annotations An insertion site on the genome Assigned it to a clone & gene

  4. Database Design (Core Schema) Chromosomes Exon Clone Gene Seq _ Chr Seq _clone Seq _gene FlankingSeq Line

  5. Programming and Database Implementation • Data parsing, insertion mapping and data loading scripts coded in Perl • Web interfaces use Perl-CGI scripts • Database implemented using MySQL, a relational DBMS

  6. ATIDB Future Enhancements • Modules for phenotype and gene expression • Integrate with gene ontology, plant ontology, trait ontology, etc.

  7. Database Design (Schema for Phenotype and Gene Expression) ATIDB core schema Line Gene Allele CVTerm Ontology Schema Phenotype Expression Environment Image Publication

  8. Acknowledgement Cold Spring Harbor Laboratory Dr. Hong Liu (former postdoc in Stein Lab) Steven Schmidt Dr. Scott Cain Other colleagues John Innes Centre, UK Dr. Mike Bevan Dr. Jonathan Clarke Other technical staff

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