Category Cross-Omics>Pathway Knowledge Bases/Databases/Tools and Genomics>Genetic Data Analysis/Tools

Abstract metaTIGER (a metabolic gene evolution resource) is a collection of 'metabolic profiles' and 'phylogenomic information' on a taxonomically diverse range of eukaryotes. Phylogenomic information is provided by 2,257 large phylogenetic trees which can be interactively explored.

High-throughput tree analysis can also be carried out to identify trees of interest, e.g. trees containing horizontal gene transfers. metaTIGER also provides novel facilities for viewing and comparing the metabolic profiles.

The prediction of enzymes and in turn an organisms metabolic profiles is based upon the program SHARKhunt. SHARKhunt is a high- throughput genome annotation program which takes genomic DNA sequence and searches it with enzyme profiles.

The enzymes profiles are based upon the alignment of the amino acids sequence of conserved regions of genes of known function.

These are used to search the genomes using a combination of two sensitive bioinformatics techniques, PSI-BLAST and Hidden Markov Models, which means distant homolog’s can be detected in highly diverged organisms.

metaTIGER provides a variety of ways of exploring and comparing these enzyme predictions, including: search functions, organism specific pathway images, comparative pathway images and the potential to compare 10's of organisms at once through table based comparison.

To accompany each of the enzyme profiles in metaTIGER is a maximum-likelihood phylogenetic tree that was produced from an alignment of the amino acid sequences.

The phylogenetic trees can be viewed interactively on the site or they can be searched with complex user designed tree queries.

To address the lack of phylogenomic information relating to eukaryotic metabolism, metaTIGER was created, using genomic information from 121 eukaryotes and 404 prokaryotes and sensitive sequence search techniques to predict the presence of metabolic enzymes.

These enzyme sequences were used to create a comprehensive database of 2,257 maximum-likelihood phylogenetic trees, some containing over 500 organisms.

The trees can be viewed using iTOL, an advanced interactive tree viewer, enabling straightforward interpretation of large trees.

Complex high-throughput tree analysis is also available through user- defined queries, allowing the rapid identification of trees of interest, e.g. containing putative HGT events.

metaTIGER also provides novel and easy-to-use facilities for viewing and comparing the metabolic networks in different organisms via highlighted pathway images and tables.

metaTIGER is demonstrated through evolutionary analysis of Plasmodium, including identification of genes horizontally transferred from chlamydia.

metaTIGER features/capabilities include:

Searching metaTIGER -- A specific eukaryote or group of eukaryotes can be searched for a particular enzyme or compound.

For all searches the user can determine the search type, the e-value cut- off, the group of the organism or the organism to search through, and the text to be searched for.

Enzyme Information Pages -- The enzyme info page contains several sections:

1) Title - which is made up of the enzymes name, ec number, and e- value.

2) BLAST - there are two (2) different BLAST options; the first runs a search against the UniProt database, the second option is a recomputed search of the NCBI's non-redundant protein database.

3) Pathway Links - a list of links that will take you to the pathways in which the enzyme occurs, where all the reactions that are predicted to occur within the organism are highlighted.

4) Data - a link to a Fasta file of the AA sequences of the hits.

5) External Links - a list of links that take you to the information pages for the enzyme in other databases.

6) Profile Trees - the phylogenetic trees of the profiles. The organisms of relevance are highlighted by a black square on the outside of the tree.

7) Additionally, provides a link called 'genome info' that gives you information about the type of genomic information that was used in the metabolic profile prediction, where it was downloaded from and when it was downloaded.

Viewing metaTIGER Pathways -- There are two ways of exploring the pathway images contained within metaTIGER. The first is to us the 'All Pathways' option that allows users to select any organism and pathway that is contained in metaTIGER.

The second option is to use the Filtered Pathways menu; this allows users to explore the pathways that are most relevant to their organism of choice.

Pathway Comparison - Images -- A pathway image that compares that pathway between two organisms can be produced.

Once an image has been viewed it will be saved on the manufacturer's server allowing it to be viewed in a faction of the time if the comparison is loaded again.

Pathway Comparison - List -- The list comparison brings with it the advantage that it can be used to compare more than two organisms at once.

You can also choose if enzymes that are Not detectable should be included in the list (enzymes are Not detectable because there is No profile for them in the manufacturer's metabolic profile prediction software).

In addition to comparing lists of 'ec numbers' as they appear in different KEGG networks that are user specified, an ec number list can be compared.

All of the text of the 'results page' links to further information about that aspect of the results (when you click-on):

1) Ec number – it opens the KEGG image of the pathway with the enzyme highlighted. This allows you to see which reaction in the map it carries out.

2) Organism name – it opens the pathway image for that organism.

3) E-value of a hit – it opens the enzyme information page for that organism and enzyme.

Phylogenetic Trees -- The phylogenetic trees are viewable on the enzyme info pages.

Only sequences with e-values less that 1.0e-30 are included in the trees as hits with e-values greater than this were found Not to contain enough phylogenetic information for accurate tree construction.

If an organism has more than one hit which is less than 1.0e-30 then only the hit with the lowest e-value is used in the tree.

Tree Searching -- The tree searching service makes use of the program PHAT which is part of the PhyloGenie package (an automated phylome generation and analysis system) to search through all of the phylogenetic trees in metaTIGER.

PHAT offers a sophisticated re-rooting technique that ensures that clades being tested do Not cross the root.

The manufacturer offers three (3) tree search options:

1) Selection String - this is a query that describes the type of HGT event that you are trying to discover. This is written using PHAT selection syntax.

2) A minimum bootstrap value - branches with bootstrap values beneath this value are ignored from the analysis.

3) E-mail address - for the results to be sent to. Data Download option -- This option allows all the SHARKhunt results which metaTIGER is based upon to be downloaded.

BLAST option -- The metaTIGER search facility allows users to search the metaTIGER sequence database with their own nucleotide or amino acid sequences.

System Requirements

Web based.


Manufacturer Web Site metaTIGER

Price Contact manufacturer.

G6G Abstract Number 20303

G6G Manufacturer Number 102833