Eggs derived from germ-line clones were collected twice

eloping a multi-level Hidden Markov Model library that is capable of classifying protein kinases into their correct functional group. The protein kinase HMM library was shown to be three times more sensitive than BLAST for identifying kinase catalytic domains. It was also shown to be more sensitive than a general Pfam model of the kinase PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19815606 catalytic domain, with the added advantage that the HMM library is capable of discriminating among protein kinase groups. The validated HMM library was applied to improve the grouplevel classification of the S. cerevisiae ePKs from 66.96% to 90.43% by classifying many of the yeast kinases previously assigned to the `Other’ group. In this article, we describe the extension of this analysis to the complete classification at the kinase group level of 43 curated eukaryotic kinomes and a web-based resource through which these annotations can be examined. In addition, we provide an interface to the HMM library, allowing for the classification of arbitrary sequences. MATERIALS AND METHODS Sequence data sources The complete translated protein coding sequences were obtained for the fungi Aspergillus fumigatus, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Candida glabrata, Cryptococcus neoformans, Debaryomyces hansenii, Kluyveromyces lactis, Magnaporthe grisea, Neurospora crassa, Phanerochaete chrysosporium, Ustilago maydis and Yarrowia lipolytica. Among the photosynthetic organisms we have included A. thaliana, the red alga Cyanidioschyzon merolae, the rice species Oryza sativa ssp. Japonica, the green algae Ostreococcus lucimarinus and Ostreococcus tauri, and the poplar tree Populus trichocarpa. The metazoan genomes include the yellow fever mosquito Aedes aegypti, the malaria mosquito vector Anopheles gambiae, the silkworm Bombyx mori, the Celgosivir biological activity common dog Canis familiaris, the early chordate Ciona intestinalis, the chicken Gallus gallus, the Rhesus macaque Macaca mulatta, the marsupial Monodelphis domestica , the fishes medaka Oryzias latipes, Takifugu rubripes and Tetraodon nigroviridis, the laboratory rat Rattus norvegicus and the chimpanzee Pan troglodytes. Finally, we have also included the amoeba Entamoeba histolytica, the diatom Thalassiosira pseudonana and the pathogenic protist Trichomonas vaginalis. The manually annotated kinomes of Caenorhabditis elegans, Dictyostelium discoideum, Drosophila melanogaster, Homo sapiens and M. musculus were downloaded from Kinbase on 28 September 2008. The manually annotated kinomes of Encephalitozoon cuniculi, Saccharomyces cerevisiae and Schyzosaccharomyces pombe had previously been manually annotated and analysed in detail. Kinase classification The predicted peptide sequences for each of the genomes were searched individually against the Kinomer v. 1.0 multi-level HMM library with the hmmpfam program of the HMMer package. Partial matches to the kinase catalytic domain were excluded through manual curation. Empirical cutoffs for association of kinase matches with each of the specific kinase groups were determined through analysis of the significance scores for the matches of the library HMMs to the well annotated kinases in Kinbase for the organisms H. sapiens, C. elegans, D. melanogaster and S. cerevisiae. The highest observed E-value for that group was taken as the cutoff for confident assignment. This web based tool allows a user to upload a sequence in any of the many sequence formats supported by EMBOSS, including the popular FASTA, GCG, PIR and Swis