An important part of such analysis is the comparison between organisms capable of comprehensive organ regeneration and those, which have lost (or suppress) this ability.
PomBase (http://www.pombase.org) has recently been established as a comprehensive model organism database that provides centralized access to information relevant to S.pombe (Wood et al., 2012).
To obtain a comprehensive and organism specific network, we extracted all reactions catalyzed by enzymes from both the central carbon metabolism and fermentation subcategories of RAST's carbohydrate metabolism group.
To assign NOG to each gene, BLAST (v 2.2.26) was performed for the protein sequences of all 2,406 genomes against the eggNOG version 4.0 database which is a comprehensive (3,686 organisms) catalog of functionally annotated orthologous groups and deals with the existing problems of determining the orthology and provides an extensive and curated resource of orthologous groups of genes.
In supporting different labs studying different organisms, a comprehensive set of model organism genome references are fully integrated to allow for flexible association notations.
With the completion of genome projects from numerous eukaryotic organisms, comprehensive studies on the mobile genetic elements have been conducted with the whole genomic sequences.
After this initial screen to identify sequences with similarity to viral genomes, the subset of sequences identified was aligned to the larger nucleotide and translated amino acid sequence databases [ 40], which include entries from a more comprehensive set of organisms.
A higher proportion of children with persistent diarrhoea tested positive for any pathogen, but the frequency of detection was also high in children without diarrhoea; across studies that tested for a comprehensive range of organisms, 65% of children with persistent diarrhoea tested positive for at least one pathogen, compared with 43% of children without diarrhoea.
Such multi-species databases, however, are rarely fully comprehensive for any one organism; for example, organism-specific gene information, such as gene expression and phenotype data is not available for searching and filtering the interaction data.
