@bio = (a..z);

bioinformatics development and consulting

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iTOL: interactive Tree Of Life

Interactive Tree Of Life is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize mid-sized tree (up to several thousand leaves). Trees can be exported to several graphical formats, both bitmap and vector based.
There are several pre-computed trees available for display, including the main Tree Of Life, described in Ciccarelli, et al., 2006. In addition to the precomputed trees, users can upload and display personal trees and data, using the 'Data upload' page or through a personal user account.

More information: Visit iTOL, PubMed link, Article (PDF)

Click the thumbnails for full size images

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iTOL user interface
The main user interface with the Tree Of Life displayed.
Circular display mode
A tree in circular mode, with a pie chart and stacked barchart datasets.
Horizontal transfers
A tree in inverted circular mode, with a stacked barchart. Green arrows correspond to horizontal gene transfers.

iPath: interactive Pathways Explorer

interactive Pathways Explorer is a web-based tool for the visualization and analysis of the metabolic pathways. The underlying global pathways map is constructed using approximately 120 KEGG pathways, and gives an overview of the complete metabolism in biological systems. Nodes in the map correspond to various chemical compounds and edges represent series of enzymatic reactions.
Various types of data can be mapped onto the default global map, changing the colors, opacity and width of any node or edge. In addition, iPath provides a set of precomputed metabolic pathway maps for various species and taxnonomic classes. All maps in iPath can be easily converted to various graphical formats.

More information: Visit iPath, PubMed link, Article (PDF)

Click the thumbnails for full size images

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iPath user interface
The main user interface of the interactive Pathways Explorer.
Map customization
Powerful data mapping tools allow easy creation of customized pathways maps.
Pathways present in fruitfly
Species restricted pathways maps are generated through mapping of orthologus proteins.

SMART: Simple Modular Architecture Research Tool

SMART allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 750 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.

More information: Visit SMART, PubMed link, Article (PDF)

Click the thumbnails for full size images

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SMART user interface
The main user interface of the Simple Modular Architecture Research Tool.
Protein domain analysis
Human tyrosine kinase TEC displayed in SMART.
Domain architecture analysis
The database was queried for proteins containing CUB and CCP domains.

iMetaWorld

iMetaworld is a web-based resource that integrates public physicochemical data (e.g. CO2 or salinity) with environmental sequencing (metagenomics) data measured in various projects. It allows, for example, to correlate gene abundances in certain samples with environmental constraints. The selection of subsets of the exponentially growing number of samples enables detailed analyses under standardized conditions (e.g. water depth of 2m) as metabolic differences seen in distinct oceans might not only be due to geografic locations, but varying environmental conditions. The resource enables to animations of time series and spatial variations. It can highlight metabolic adaptations that are more due to nutrition conditions and those that require other life style adaptations (temperature, UV etc.).

More information: not publicly available at the moment

Click the thumbnails for full size images

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iMetaWorld user interface
Average January oxygen level at sea surface is displayed. The interface is still under heavy development.
Searching for sampling sites
Global Ocean Survey sampling points are displayed. Dot size is proportional to the number of sequences present in the dataset.
Sampling site details
Detailed information about a specific site is displayed. An interactive metabolic pathways map shows the levels of over and under represented KEGG maps.

Other projects and tools

Other software: