Imdb a generic insertional mutagenesis database
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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

IMDB: A Generic Insertional Mutagenesis Database

Xiaokang Pan and Lincoln Stein

Cold Spring Harbor Laboratory


Objectives
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


Insertion mapping
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


Database design core schema
Database Design (Core Schema)

Chromosomes

Exon

Clone

Gene

Seq

_

Chr

Seq

_clone

Seq

_gene

FlankingSeq

Line


Programming and database implementation
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


Atidb future enhancements
ATIDB Future Enhancements

  • Modules for phenotype and gene expression

  • Integrate with gene ontology, plant ontology, trait ontology, etc.


Database Design

(Schema for Phenotype and Gene Expression)

ATIDB

core schema

Line

Gene

Allele

CVTerm

Ontology

Schema

Phenotype

Expression

Environment

Image

Publication


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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