SIB Microbe Browser

Category Genomics>Genetic Data Analysis/Tools

Abstract The Microbe Browser is a web server providing comparative microbial genomics data.

Designed primarily for biomedical researchers, the Microbe Browser provides an easy-to-use interactive view, allowing you to visualize gene predictions, orthology and synteny relationships and to navigate across databases.

It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology (GO) and the Orthologs Matrix Project (OMA) database, displayed along with gene predictions from five (5) software packages.

The Microbe Browser is updated daily from the source databases and includes all completely sequenced bacterial and archaeal genomes. The data is displayed in an easy-to-use, interactive website based on Ensembl software.

Microbe Browser Methods --

Source data is retrieved daily from primary public servers.

Integr8 and Genome Reviews are the source of genome data, including curated gene sets and annotation and cross-references to UniProtKB, InterPro, Gene Ontology (GO) and the Protein Data Bank (PDB).

GenBank and RefSeq are the source of NCBI cross-references (RefSeq accession, GeneID and GI number).

The OMA database provides 'orthology predictions' for pairs of genes. Pre-computed gene predictions from:

1) GLIMMER - (The GLIMMER system for microbial gene identification finds approximately 97-98% of all genes in a genome when compared with published annotation);

2) GeneMark;

3) GeneMarkHMM - [GeneMark can be used for whole genome analysis as well as for the local analysis of a particular gene and its surrounding regions;

GeneMark.HMM makes use of Hidden Markov models (HMM) to find the transition points (boundaries) between protein coding states and non- coding states and can be efficiently used for larger genome sequences.

These methods can be used in conjunction with each other for a higher sensitivity of gene detection].

4) Prodigal packages are provided by the National Center for Biotechnology Information (NCBI) -

[Prodigal (Prokaryotic Dynamic Programming Gene-finding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee]; and

5) Predictions by the EasyGene method are downloaded from the EasyGene web site - [EasyGene estimates the statistical significance of a predicted gene. The gene finder is based on a Hidden Markov model (HMM) that is automatically estimated for a new genome -

EasyGene produces a list of predicted genes for a chosen prokaryotic genome. Each prediction is attributed with a significance score (R- value) indicating how likely it is to be just a non-coding open reading frame rather than a real gene].

The ‘Genome Reviews’ data is used as a reference because it incorporates substantial automatic and manual annotation from the gold standard UniProtKB knowledgebase (KB).

Cross-references from GenBank and RefSeq genes are merged into Genome Reviews records based on the position of the 3'-end of the genes.

This allows you to correctly map Not only genes for which No cross- references exist between the databases, but also those for which the 5'- end (start site) that has been possibly changed by UniProtKB curators.

Microbe Browser Usage --

The Microbe Browser home page is used for organism selection and search term input, which can be a gene name or a cross-reference to any of the source databases.

Several view pages are available, the three (3) most informative are detailed below.

The user can easily navigate across those pages and extensive detailed online help is available.

The 'gene report' page integrates data on ‘gene sequence’ and annotation, orthologs and cross-references to the major biological databases.

The 'chromosome view' pages display the original genome annotation submitted in the DNA Data Bank of Japan (DDBJ)/EMBL/GenBank source databases, the modified annotation from UniProtKB (via Genome Reviews) and the gene predictions of several popular software packages.

The 'chromosome comparison' pages display regions surrounding orthologous genes in two (2) or more organisms, highlighting orthology relationships between them, and reveal cases of synteny (co-localized orthologs).

This display scales up to comparing a few species with detailed positional information, while specialized software is recommended to visualize synteny across dozens of species in a summarized display - (SynteBase/SynteView - a tool to visualize gene order conservation in prokaryotic genomes.

SynteBase answers queries about gene order conservation and SynteView visualizes the obtained results in a flexible and advanced way which provides a comparative overview of the conserved synteny in a large number of genomes, whatever their taxonomic distances).

Data Displays (view pages) available are as follows:

ContigView; DomainView;FastaView; FeatureView; GeneSeqView; GeneView; GOView; KaryoView; MapView; MultiContigView; ProteinView; and TransView.

Note: For software developers, programmatic access to the 'orthology relationships' is available via web services through the OMA Application Programming Interfaces (APIs)

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site SIB Microbe Browser

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G6G Abstract Number 20496

G6G Manufacturer Number 104117