What are they ?

BioDecoders are state-of-the-art pipelines for the annotation of proteome biosequences: we have tools for prokaryotic and eukaryotic organisms. A specialized tool has been built for G-Protein Coupled Receptor proteins (GPCRs). The annotation results are published in multiple presentation formats (the Proteome Atlases) such as hyper-linked PDF ebooks for reading and printing, HTML pages for web publishing, XML for data interchange and are available as annotated databases.

Angler

Angler consists of two modules, one suited for Prokaryotes (Angler-PRO) and the other for Eukaryotes (Angler-EU). They are based on a hierarchical combination of different BioDec Tools.

Angler-PRO is based on the HUNTER method by Casadio et al. (Protein Sci. 12, 2003, 1158), that classifies gram-negative proteome sequences into nine different classes, including among the others, the all-beta membrane proteins and the soluble secreted proteins, that are the most relevant to vaccine development. Angler-PRO can be roughly described as follows: the first, and most demanding, Angler step is the construction of a protein profile for each protein sequence; then, an extremely fast classification step is executed, dividing the proteome into the nine different classes; next all sequences are fed into a robust, fast fold recognition protocol to highlight the putative structural homologues of the classified sequence. The Angler classification is highly reliable: as an example, Angler performance has been measured around 85% accuracy and 75% coverage of the "Outer Membrane Protein" class on E. coli K12.

Angler-EU shares with Angler-PRO the same philosophy. However it is based on a different pipeline, with remarkably different end classes. This is due to the several different organelles typical of Eukaryotic cell, requiring subtle and specific calibration ofthe classification algorithms.

Cribrum

This is a specific tool that searches for GPCR sequences in proteomes. Cribrum classifies the putative GPCR sequences in probable family or subfamilies at different tree-depth, according to the level of knowledge and availability of the different GPCR subfamily members. These are derived from a newly consistent annotation of the loops and transmembrane segments for the G-Protein Coupled Receptor proteins found in public (or custom) databases and reclassified according to a BioDec procedure.

How do you use them

The best way to use the BioDecoders is through BioDec's Bioinformation Management Systems, but they can also be used independently: in this latter case, you should probably try to integrate each BioDecoder with your own enterprise systems. Otherwise, you can just use the annotation results, either as documentation or as annotated databases.