MetaGene Server

Background

MetaGene is a utility created to use sequence analysis packages currently available on the web to create an environment for exhaustive analysis of predicted gene features. MetaGene is a long term project whose goals of on-line sequence analysis, feature annotation and optimization will provide a framework for exhaustive review and analysis.

Genetic analysis of large sequences can be executed using a wide variety of gene feature prediction engines available on the WEB. A gene feature identification tool (MetaGene) was created to take advantage of these systems and create an object-based comprehensive annotation system. This tool has proven effective in consolidating all predicted features in the sequence into a unifying framework thereby allowing further studies to be conducted such as the identification of apparent classification of gene features via cluster analysis applied to large collections of known genes. A database of known genes was created to support MetaGene including sequences, known gene features, and predicted gene features collated by MetaGene. MetaGene allows users to submit a single sequence or a collection of sequences simultaneously to a large collection of prediction engines (N=9). Results are standardized and presented in two formats: raw output and consolidated annotation for easy dissemination and "optimized" prediction. Optimized prediction will attach confidence measures to each predicted gene feature. MetaGene and the supporting database (ORACLE) were designed to support the integration of other sequence analysis applications whether off or on-site. Object-Oriented (OO) methodology was employed to develop a highly modularized, robust environment that has proven stable and effective.

How to use MetaGene

MetaGene offers a friendly interactive frondend, you can summit unknown sequences either by paste to the blank place provided, or just browse files in your locality. Several options are provided to give a flexible choice for different users. The predicted results could be retrieved either via email or MG query ID.

MetaGene has default choice for each of nine search engines, users are easy to choose other options.

MetaGene also gives a graphical and animated annotation result. Based on the optimization of all the results, MetaGene could give its own predicted values at optimal threshold.

Annotation/Analysis

Below is an example of annotated search results for sequence HSSPN1AG from ALLSEQ.