Genome Annotator light(GAL): An integrated virtual machine for genome analysis and visualization

ARIJIT PANDACSIR-SENIOR RESEARCH FELLOW

CSIR-INDIAN INSTITUTE OF CHEMICAL BIOLOGY

Introduction

A tool to visualize and analyse genome or group of genome Analytical Part

Comparative genomics Signalp Secretome Interproscan

Visualization Part Genome Browser Gene details Synteny viewer GFF visualization

Background

MySQL database Database schema is based on Genome Unified schema(GUS) with huge

makeover Perl/CGI/GD, PHP, Javascript , Ajax is used in the front end

Config file

No Annotation : Simple Genome Fasta file

Minimal Annotation:Genome Fasta + GFF + Blast

Product File

Complete Annotation:Genome Fasta+GFF+Blast+ Interpro+signalp+interpro +

secretome etc

User InformationDatabase Credentials

Check all the user provided

information

Failed

Pass

Check &

create schema

Work Flow

Gene Prediction

Run BLAST

Create dummy product file

Run Other annotation

tool

Create product file

Parsers

Fully Integrated Web based Database

No Annotation

Minimal Annotation

Complete Annotation

YES

No, Later

Data Upload

Shared Resources

Config FileINI Format

[Section]Name = value

Key Features

Genome Browser GFF visualization Gene Details Page Comparative Genomics information Database query is available to fetch information Version control is there to upload different version of same genome

Application

We have implemented GAL in two type of genome datasets:1. Oomycete Genomes: Eumicrobedb.org2. Cyanobacterial Genomes : Bgagenomics.iicb.res.in

Eumicrobedb

26 Genomes

Browser Page:

Gene Details Page

Synteny Viewer

BgagenomicsDB

69 Genomes

Summary

A package to visualize and analyse a genome or a group of genome It takes only 8-10 minutes time to upload a complete genome if

complete annotation is provided It works for both eukaryote and prokaryote genomes Version control is present in the tool to upload different version of same

genome

Acknowledgement

Council of Scientific & Industrial Research (CSIR), Government of India Department of Biotechnology , Government of India

Lab members

Akash GuptaDiya SenSubhadeep DasAbhishek DasMathu Malar CArup GhoshGyan Prakash MishraMadhu Madduluri

Project InvestigatorSucheta Tripathy

Prof. Brett Tyler,Oregon State University

Special Thanks